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Sample records for discovery decodes cis-regulatory

  1. SMCis: An Effective Algorithm for Discovery of Cis-Regulatory Modules

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    Guo, Haitao; Huo, Hongwei; Yu, Qiang

    2016-01-01

    The discovery of cis-regulatory modules (CRMs) is a challenging problem in computational biology. Limited by the difficulty of using an HMM to model dependent features in transcriptional regulatory sequences (TRSs), the probabilistic modeling methods based on HMMs cannot accurately represent the distance between regulatory elements in TRSs and are cumbersome to model the prevailing dependencies between motifs within CRMs. We propose a probabilistic modeling algorithm called SMCis, which builds a more powerful CRM discovery model based on a hidden semi-Markov model. Our model characterizes the regulatory structure of CRMs and effectively models dependencies between motifs at a higher level of abstraction based on segments rather than nucleotides. Experimental results on three benchmark datasets indicate that our method performs better than the compared algorithms. PMID:27637070

  2. A primer on regression methods for decoding cis-regulatory logic

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    Das, Debopriya; Pellegrini, Matteo; Gray, Joe W.

    2009-03-03

    The rapidly emerging field of systems biology is helping us to understand the molecular determinants of phenotype on a genomic scale [1]. Cis-regulatory elements are major sequence-based determinants of biological processes in cells and tissues [2]. For instance, during transcriptional regulation, transcription factors (TFs) bind to very specific regions on the promoter DNA [2,3] and recruit the basal transcriptional machinery, which ultimately initiates mRNA transcription (Figure 1A). Learning cis-Regulatory Elements from Omics Data A vast amount of work over the past decade has shown that omics data can be used to learn cis-regulatory logic on a genome-wide scale [4-6]--in particular, by integrating sequence data with mRNA expression profiles. The most popular approach has been to identify over-represented motifs in promoters of genes that are coexpressed [4,7,8]. Though widely used, such an approach can be limiting for a variety of reasons. First, the combinatorial nature of gene regulation is difficult to explicitly model in this framework. Moreover, in many applications of this approach, expression data from multiple conditions are necessary to obtain reliable predictions. This can potentially limit the use of this method to only large data sets [9]. Although these methods can be adapted to analyze mRNA expression data from a pair of biological conditions, such comparisons are often confounded by the fact that primary and secondary response genes are clustered together--whereas only the primary response genes are expected to contain the functional motifs [10]. A set of approaches based on regression has been developed to overcome the above limitations [11-32]. These approaches have their foundations in certain biophysical aspects of gene regulation [26,33-35]. That is, the models are motivated by the expected transcriptional response of genes due to the binding of TFs to their promoters. While such methods have gathered popularity in the computational domain

  3. Computational discovery of soybean promoter cis-regulatory elements for the construction of soybean cyst nematode inducible synthetic promoters

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    Computational methods offer great hope but limited accuracy in the prediction of functional cis-regulatory elements; improvements are needed to enable synthetic promoter design. We applied an ensemble strategy for de novo soybean cyst nematode (SCN)-inducible motif discovery among promoters of 18 co...

  4. Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

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    van Helden Jacques

    2008-01-01

    Full Text Available Abstract Background The detection of conserved motifs in promoters of orthologous genes (phylogenetic footprints has become a common strategy to predict cis-acting regulatory elements. Several software tools are routinely used to raise hypotheses about regulation. However, these tools are generally used as black boxes, with default parameters. A systematic evaluation of optimal parameters for a footprint discovery strategy can bring a sizeable improvement to the predictions. Results We evaluate the performances of a footprint discovery approach based on the detection of over-represented spaced motifs. This method is particularly suitable for (but not restricted to Bacteria, since such motifs are typically bound by factors containing a Helix-Turn-Helix domain. We evaluated footprint discovery in 368 Escherichia coli K12 genes with annotated sites, under 40 different combinations of parameters (taxonomical level, background model, organism-specific filtering, operon inference. Motifs are assessed both at the levels of correctness and significance. We further report a detailed analysis of 181 bacterial orthologs of the LexA repressor. Distinct motifs are detected at various taxonomical levels, including the 7 previously characterized taxon-specific motifs. In addition, we highlight a significantly stronger conservation of half-motifs in Actinobacteria, relative to Firmicutes, suggesting an intermediate state in specificity switching between the two Gram-positive phyla, and thereby revealing the on-going evolution of LexA auto-regulation. Conclusion The footprint discovery method proposed here shows excellent results with E. coli and can readily be extended to predict cis-acting regulatory signals and propose testable hypotheses in bacterial genomes for which nothing is known about regulation.

  5. Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules.

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    Todd P Michael

    2008-02-01

    Full Text Available Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.

  6. Cis-regulatory mutations in human disease.

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    Epstein, Douglas J

    2009-07-01

    Cis-acting regulatory sequences are required for the proper temporal and spatial control of gene expression. Variation in gene expression is highly heritable and a significant determinant of human disease susceptibility. The diversity of human genetic diseases attributed, in whole or in part, to mutations in non-coding regulatory sequences is on the rise. Improvements in genome-wide methods of associating genetic variation with human disease and predicting DNA with cis-regulatory potential are two of the major reasons for these recent advances. This review will highlight select examples from the literature that have successfully integrated genetic and genomic approaches to uncover the molecular basis by which cis-regulatory mutations alter gene expression and contribute to human disease. The fine mapping of disease-causing variants has led to the discovery of novel cis-acting regulatory elements that, in some instances, are located as far away as 1.5 Mb from the target gene. In other cases, the prior knowledge of the regulatory landscape surrounding the gene of interest aided in the selection of enhancers for mutation screening. The success of these studies should provide a framework for following up on the large number of genome-wide association studies that have identified common variants in non-coding regions of the genome that associate with increased risk of human diseases including, diabetes, autism, Crohn's, colorectal cancer, and asthma, to name a few.

  7. Integration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in Arabidopsis.

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    Koschmann, Jeannette; Machens, Fabian; Becker, Marlies; Niemeyer, Julia; Schulze, Jutta; Bülow, Lorenz; Stahl, Dietmar J; Hehl, Reinhard

    2012-09-01

    A combination of bioinformatic tools, high-throughput gene expression profiles, and the use of synthetic promoters is a powerful approach to discover and evaluate novel cis-sequences in response to specific stimuli. With Arabidopsis (Arabidopsis thaliana) microarray data annotated to the PathoPlant database, 732 different queries with a focus on fungal and oomycete pathogens were performed, leading to 510 up-regulated gene groups. Using the binding site estimation suite of tools, BEST, 407 conserved sequence motifs were identified in promoter regions of these coregulated gene sets. Motif similarities were determined with STAMP, classifying the 407 sequence motifs into 37 families. A comparative analysis of these 37 families with the AthaMap, PLACE, and AGRIS databases revealed similarities to known cis-elements but also led to the discovery of cis-sequences not yet implicated in pathogen response. Using a parsley (Petroselinum crispum) protoplast system and a modified reporter gene vector with an internal transformation control, 25 elicitor-responsive cis-sequences from 10 different motif families were identified. Many of the elicitor-responsive cis-sequences also drive reporter gene expression in an Agrobacterium tumefaciens infection assay in Nicotiana benthamiana. This work significantly increases the number of known elicitor-responsive cis-sequences and demonstrates the successful integration of a diverse set of bioinformatic resources combined with synthetic promoter analysis for data mining and functional screening in plant-pathogen interaction.

  8. Statistical significance of cis-regulatory modules

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    Smith Andrew D

    2007-01-01

    Full Text Available Abstract Background It is becoming increasingly important for researchers to be able to scan through large genomic regions for transcription factor binding sites or clusters of binding sites forming cis-regulatory modules. Correspondingly, there has been a push to develop algorithms for the rapid detection and assessment of cis-regulatory modules. While various algorithms for this purpose have been introduced, most are not well suited for rapid, genome scale scanning. Results We introduce methods designed for the detection and statistical evaluation of cis-regulatory modules, modeled as either clusters of individual binding sites or as combinations of sites with constrained organization. In order to determine the statistical significance of module sites, we first need a method to determine the statistical significance of single transcription factor binding site matches. We introduce a straightforward method of estimating the statistical significance of single site matches using a database of known promoters to produce data structures that can be used to estimate p-values for binding site matches. We next introduce a technique to calculate the statistical significance of the arrangement of binding sites within a module using a max-gap model. If the module scanned for has defined organizational parameters, the probability of the module is corrected to account for organizational constraints. The statistical significance of single site matches and the architecture of sites within the module can be combined to provide an overall estimation of statistical significance of cis-regulatory module sites. Conclusion The methods introduced in this paper allow for the detection and statistical evaluation of single transcription factor binding sites and cis-regulatory modules. The features described are implemented in the Search Tool for Occurrences of Regulatory Motifs (STORM and MODSTORM software.

  9. Computational identification of new structured cis-regulatory elements in the 3'-untranslated region of human protein coding genes.

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    Chen, Xiaowei Sylvia; Brown, Chris M

    2012-10-01

    Messenger ribonucleic acids (RNAs) contain a large number of cis-regulatory RNA elements that function in many types of post-transcriptional regulation. These cis-regulatory elements are often characterized by conserved structures and/or sequences. Although some classes are well known, given the wide range of RNA-interacting proteins in eukaryotes, it is likely that many new classes of cis-regulatory elements are yet to be discovered. An approach to this is to use computational methods that have the advantage of analysing genomic data, particularly comparative data on a large scale. In this study, a set of structural discovery algorithms was applied followed by support vector machine (SVM) classification. We trained a new classification model (CisRNA-SVM) on a set of known structured cis-regulatory elements from 3'-untranslated regions (UTRs) and successfully distinguished these and groups of cis-regulatory elements not been strained on from control genomic and shuffled sequences. The new method outperformed previous methods in classification of cis-regulatory RNA elements. This model was then used to predict new elements from cross-species conserved regions of human 3'-UTRs. Clustering of these elements identified new classes of potential cis-regulatory elements. The model, training and testing sets and novel human predictions are available at: http://mRNA.otago.ac.nz/CisRNA-SVM.

  10. Abundant raw material for cis-regulatory evolution in humans

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    Rockman, Matthew V.; Wray, Gregory A.

    2002-01-01

    Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (human phenotypic variation.

  11. Abundant raw material for cis-regulatory evolution in humans

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    Rockman, Matthew V.; Wray, Gregory A.

    2002-01-01

    Changes in gene expression and regulation--due in particular to the evolution of cis-regulatory DNA sequences--may underlie many evolutionary changes in phenotypes, yet little is known about the distribution of such variation in populations. We present in this study the first survey of experimentally validated functional cis-regulatory polymorphism. These data are derived from more than 140 polymorphisms involved in the regulation of 107 genes in Homo sapiens, the eukaryote species with the most available data. We find that functional cis-regulatory variation is widespread in the human genome and that the consequent variation in gene expression is twofold or greater for 63% of the genes surveyed. Transcription factor-DNA interactions are highly polymorphic, and regulatory interactions have been gained and lost within human populations. On average, humans are heterozygous at more functional cis-regulatory sites (>16,000) than at amino acid positions (human phenotypic variation.

  12. The role of cis regulatory evolution in maize domestication.

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    Lemmon, Zachary H; Bukowski, Robert; Sun, Qi; Doebley, John F

    2014-11-01

    Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes) show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues.

  13. The Role of cis Regulatory Evolution in Maize Domestication

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    Lemmon, Zachary H.; Bukowski, Robert; Sun, Qi; Doebley, John F.

    2014-01-01

    Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem). Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes) show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues. PMID:25375861

  14. The role of cis regulatory evolution in maize domestication.

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    Zachary H Lemmon

    2014-11-01

    Full Text Available Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem. Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues.

  15. The role of cis regulatory evolution in maize domestication.

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    Zachary H Lemmon

    2014-11-01

    Full Text Available Gene expression differences between divergent lineages caused by modification of cis regulatory elements are thought to be important in evolution. We assayed genome-wide cis and trans regulatory differences between maize and its wild progenitor, teosinte, using deep RNA sequencing in F1 hybrid and parent inbred lines for three tissue types (ear, leaf and stem. Pervasive regulatory variation was observed with approximately 70% of ∼17,000 genes showing evidence of regulatory divergence between maize and teosinte. However, many fewer genes (1,079 genes show consistent cis differences with all sampled maize and teosinte lines. For ∼70% of these 1,079 genes, the cis differences are specific to a single tissue. The number of genes with cis regulatory differences is greatest for ear tissue, which underwent a drastic transformation in form during domestication. As expected from the domestication bottleneck, maize possesses less cis regulatory variation than teosinte with this deficit greatest for genes showing maize-teosinte cis regulatory divergence, suggesting selection on cis regulatory differences during domestication. Consistent with selection on cis regulatory elements, genes with cis effects correlated strongly with genes under positive selection during maize domestication and improvement, while genes with trans regulatory effects did not. We observed a directional bias such that genes with cis differences showed higher expression of the maize allele more often than the teosinte allele, suggesting domestication favored up-regulation of gene expression. Finally, this work documents the cis and trans regulatory changes between maize and teosinte in over 17,000 genes for three tissues.

  16. A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model

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    Haitao Guo

    2017-01-01

    Full Text Available The discovery of cis-regulatory modules (CRMs is the key to understanding mechanisms of transcription regulation. Since CRMs have specific regulatory structures that are the basis for the regulation of gene expression, how to model the regulatory structure of CRMs has a considerable impact on the performance of CRM identification. The paper proposes a CRM discovery algorithm called ComSPS. ComSPS builds a regulatory structure model of CRMs based on HMM by exploring the rules of CRM transcriptional grammar that governs the internal motif site arrangement of CRMs. We test ComSPS on three benchmark datasets and compare it with five existing methods. Experimental results show that ComSPS performs better than them.

  17. Parallel evolution of chordate cis-regulatory code for development.

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    Laura Doglio

    2013-11-01

    Full Text Available Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs, yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations.

  18. Overview Article: Identifying transcriptional cis-regulatory modules in animal genomes

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    Suryamohan, Kushal; Halfon, Marc S.

    2014-01-01

    Gene expression is regulated through the activity of transcription factors and chromatin modifying proteins acting on specific DNA sequences, referred to as cis-regulatory elements. These include promoters, located at the transcription initiation sites of genes, and a variety of distal cis-regulatory modules (CRMs), the most common of which are transcriptional enhancers. Because regulated gene expression is fundamental to cell differentiation and acquisition of new cell fates, identifying, characterizing, and understanding the mechanisms of action of CRMs is critical for understanding development. CRM discovery has historically been challenging, as CRMs can be located far from the genes they regulate, have few readily-identifiable sequence characteristics, and for many years were not amenable to high-throughput discovery methods. However, the recent availability of complete genome sequences and the development of next-generation sequencing methods has led to an explosion of both computational and empirical methods for CRM discovery in model and non-model organisms alike. Experimentally, CRMs can be identified through chromatin immunoprecipitation directed against transcription factors or histone post-translational modifications, identification of nucleosome-depleted “open” chromatin regions, or sequencing-based high-throughput functional screening. Computational methods include comparative genomics, clustering of known or predicted transcription factor binding sites, and supervised machine-learning approaches trained on known CRMs. All of these methods have proven effective for CRM discovery, but each has its own considerations and limitations, and each is subject to a greater or lesser number of false-positive identifications. Experimental confirmation of predictions is essential, although shortcomings in current methods suggest that additional means of validation need to be developed. PMID:25704908

  19. Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence.

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    Wittkopp, Patricia J; Kalay, Gizem

    2011-12-06

    Cis-regulatory sequences, such as enhancers and promoters, control development and physiology by regulating gene expression. Mutations that affect the function of these sequences contribute to phenotypic diversity within and between species. With many case studies implicating divergent cis-regulatory activity in phenotypic evolution, researchers have recently begun to elucidate the genetic and molecular mechanisms that are responsible for cis-regulatory divergence. Approaches include detailed functional analysis of individual cis-regulatory elements and comparing mechanisms of gene regulation among species using the latest genomic tools. Despite the limited number of mechanistic studies published to date, this work shows how cis-regulatory activity can diverge and how studies of cis-regulatory divergence can address long-standing questions about the genetic mechanisms of phenotypic evolution.

  20. Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora.

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    Steige, Kim A; Laenen, Benjamin; Reimegård, Johan; Scofield, Douglas G; Slotte, Tanja

    2017-01-31

    Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species.

  1. The cis-regulatory logic of the mammalian photoreceptor transcriptional network.

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    Timothy H-C Hsiau

    Full Text Available The photoreceptor cells of the retina are subject to a greater number of genetic diseases than any other cell type in the human body. The majority of more than 120 cloned human blindness genes are highly expressed in photoreceptors. In order to establish an integrative framework in which to understand these diseases, we have undertaken an experimental and computational analysis of the network controlled by the mammalian photoreceptor transcription factors, Crx, Nrl, and Nr2e3. Using microarray and in situ hybridization datasets we have produced a model of this network which contains over 600 genes, including numerous retinal disease loci as well as previously uncharacterized photoreceptor transcription factors. To elucidate the connectivity of this network, we devised a computational algorithm to identify the photoreceptor-specific cis-regulatory elements (CREs mediating the interactions between these transcription factors and their target genes. In vivo validation of our computational predictions resulted in the discovery of 19 novel photoreceptor-specific CREs near retinal disease genes. Examination of these CREs permitted the definition of a simple cis-regulatory grammar rule associated with high-level expression. To test the generality of this rule, we used an expanded form of it as a selection filter to evolve photoreceptor CREs from random DNA sequences in silico. When fused to fluorescent reporters, these evolved CREs drove strong, photoreceptor-specific expression in vivo. This study represents the first systematic identification and in vivo validation of CREs in a mammalian neuronal cell type and lays the groundwork for a systems biology of photoreceptor transcriptional regulation.

  2. Identifying cis-regulatory sequences by word profile similarity.

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    Garmay Leung

    Full Text Available BACKGROUND: Recognizing regulatory sequences in genomes is a continuing challenge, despite a wealth of available genomic data and a growing number of experimentally validated examples. METHODOLOGY/PRINCIPAL FINDINGS: We discuss here a simple approach to search for regulatory sequences based on the compositional similarity of genomic regions and known cis-regulatory sequences. This method, which is not limited to searching for predefined motifs, recovers sequences known to be under similar regulatory control. The words shared by the recovered sequences often correspond to known binding sites. Furthermore, we show that although local word profile clustering is predictive for the regulatory sequences involved in blastoderm segmentation, local dissimilarity is a more universal feature of known regulatory sequences in Drosophila. CONCLUSIONS/SIGNIFICANCE: Our method leverages sequence motifs within a known regulatory sequence to identify co-regulated sequences without explicitly defining binding sites. We also show that regulatory sequences can be distinguished from surrounding sequences by local sequence dissimilarity, a novel feature in identifying regulatory sequences across a genome. Source code for WPH-finder is available for download at http://rana.lbl.gov/downloads/wph.tar.gz.

  3. Changes in Cis-regulatory Elements during Morphological Evolution

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    Yu-Lee Paul

    2012-10-01

    Full Text Available How have animals evolved new body designs (morphological evolution? This requires explanations both for simple morphological changes, such as differences in pigmentation and hair patterns between different Drosophila populations and species, and also for more complex changes, such as differences in the forelimbs of mice and bats, and the necks of amphibians and reptiles. The genetic changes and pathways involved in these evolutionary steps require identification. Many, though not all, of these events occur by changes in cis-regulatory (enhancer elements within developmental genes. Enhancers are modular, each affecting expression in only one or a few tissues. Therefore it is possible to add, remove or alter an enhancer without producing changes in multiple tissues, and thereby avoid widespread (pleiotropic deleterious effects. Ideally, for a given step in morphological evolution it is necessary to identify (i the change in phenotype, (ii the changes in gene expression, (iii the DNA region, enhancer or otherwise, affected, (iv the mutation involved, (v the nature of the transcription or other factors that bind to this site. In practice these data are incomplete for most of the published studies upon morphological evolution. Here, the investigations are categorized according to how far these analyses have proceeded.

  4. Computational methods for the detection of cis-regulatory modules.

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    Van Loo, Peter; Marynen, Peter

    2009-09-01

    Metazoan transcription regulation occurs through the concerted action of multiple transcription factors that bind co-operatively to cis-regulatory modules (CRMs). The annotation of these key regulators of transcription is lagging far behind the annotation of the transcriptome itself. Here, we give an overview of existing computational methods to detect these CRMs in metazoan genomes. We subdivide these methods into three classes: CRM scanners screen sequences for CRMs based on predefined models that often consist of multiple position weight matrices (PWMs). CRM builders construct models of similar CRMs controlling a set of co-regulated or co-expressed genes. CRM genome screeners screen sequences or complete genomes for CRMs as homotypic or heterotypic clusters of binding sites for any combination of transcription factors. We believe that CRM scanners are currently the most advanced methods, although their applicability is limited. Finally, we argue that CRM builders that make use of PWM libraries will benefit greatly from future advances and will prove to be most instrumental for the annotation of regulatory regions in metazoan genomes.

  5. Using hexamers to predict cis-regulatory motifs in Drosophila

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    Kibler Dennis

    2005-10-01

    Full Text Available Abstract Background Cis-regulatory modules (CRMs are short stretches of DNA that help regulate gene expression in higher eukaryotes. They have been found up to 1 megabase away from the genes they regulate and can be located upstream, downstream, and even within their target genes. Due to the difficulty of finding CRMs using biological and computational techniques, even well-studied regulatory systems may contain CRMs that have not yet been discovered. Results We present a simple, efficient method (HexDiff based only on hexamer frequencies of known CRMs and non-CRM sequence to predict novel CRMs in regulatory systems. On a data set of 16 gap and pair-rule genes containing 52 known CRMs, predictions made by HexDiff had a higher correlation with the known CRMs than several existing CRM prediction algorithms: Ahab, Cluster Buster, MSCAN, MCAST, and LWF. After combining the results of the different algorithms, 10 putative CRMs were identified and are strong candidates for future study. The hexamers used by HexDiff to distinguish between CRMs and non-CRM sequence were also analyzed and were shown to be enriched in regulatory elements. Conclusion HexDiff provides an efficient and effective means for finding new CRMs based on known CRMs, rather than known binding sites.

  6. A Cis-Regulatory Map of the Drosophila Genome

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    Nègre, Nicolas; Brown, Christopher D.; Ma, Lijia; Bristow, Christopher Aaron; Miller, Steven W.; Wagner, Ulrich; Kheradpour, Pouya; Eaton, Matthew L.; Loriaux, Paul; Sealfon, Rachel; Li, Zirong; Ishii, Haruhiko; Spokony, Rebecca F.; Chen, Jia; Hwang, Lindsay; Cheng, Chao; Auburn, Richard P.; Davis, Melissa B.; Domanus, Marc; Shah, Parantu K.; Morrison, Carolyn A.; Zieba, Jennifer; Suchy, Sarah; Senderowicz, Lionel; Victorsen, Alec; Bild, Nicholas A.; Grundstad, A. Jason; Hanley, David; MacAlpine, David M.; Mannervik, Mattias; Venken, Koen; Bellen, Hugo; White, Robert; Russell, Steven; Grossman, Robert L.; Ren, Bing; Gerstein, Mark; Posakony, James W.; Kellis, Manolis; White, Kevin P.

    2011-01-01

    Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide 1,2 has successfully identified specific subtypes of regulatory elements 3. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb-Response Elements 4, chromatin states 5, transcription factor binding sites (TFBS) 6–9, PolII regulation 8, and insulator elements 10; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome based on more than 300 chromatin immuno-precipitation (ChIP) datasets for eight chromatin features, five histone deacetylases (HDACs) and thirty-eight site-specific transcription factors (TFs) at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and we validated a subset of predictions for promoters, enhancers, and insulators in vivo. We also identified nearly 2,000 genomic regions of dense TF binding associated with chromatin activity and accessibility. We discovered hundreds of new TF co-binding relationships and defined a TF network with over 800 potential regulatory relationships. PMID:21430782

  7. Favorable genomic environments for cis-regulatory evolution: A novel theoretical framework.

    Science.gov (United States)

    Maeso, Ignacio; Tena, Juan J

    2016-09-01

    Cis-regulatory changes are arguably the primary evolutionary source of animal morphological diversity. With the recent explosion of genome-wide comparisons of the cis-regulatory content in different animal species is now possible to infer general principles underlying enhancer evolution. However, these studies have also revealed numerous discrepancies and paradoxes, suggesting that the mechanistic causes and modes of cis-regulatory evolution are still not well understood and are probably much more complex than generally appreciated. Here, we argue that the mutational mechanisms and genomic regions generating new regulatory activities must comply with the constraints imposed by the molecular properties of cis-regulatory elements (CREs) and the organizational features of long-range chromatin interactions. Accordingly, we propose a new integrative evolutionary framework for cis-regulatory evolution based on two major premises for the origin of novel enhancer activity: (i) an accessible chromatin environment and (ii) compatibility with the 3D structure and interactions of pre-existing CREs. Mechanisms and DNA sequences not fulfilling these premises, will be less likely to have a measurable impact on gene expression and as such, will have a minor contribution to the evolution of gene regulation. Finally, we discuss current comparative cis-regulatory data under the light of this new evolutionary model, and propose that the two most prominent mechanisms for the evolution of cis-regulatory changes are the overprinting of ancestral CREs and the exaptation of transposable elements.

  8. Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells.

    Science.gov (United States)

    Freire-Pritchett, Paula; Schoenfelder, Stefan; Várnai, Csilla; Wingett, Steven W; Cairns, Jonathan; Collier, Amanda J; García-Vílchez, Raquel; Furlan-Magaril, Mayra; Osborne, Cameron S; Fraser, Peter; Rugg-Gunn, Peter J; Spivakov, Mikhail

    2017-03-23

    Long-range cis-regulatory elements such as enhancers coordinate cell-specific transcriptional programmes by engaging in DNA looping interactions with target promoters. Deciphering the interplay between the promoter connectivity and activity of cis-regulatory elements during lineage commitment is crucial for understanding developmental transcriptional control. Here, we use Promoter Capture Hi-C to generate a high-resolution atlas of chromosomal interactions involving ~22,000 gene promoters in human pluripotent and lineage-committed cells, identifying putative target genes for known and predicted enhancer elements. We reveal extensive dynamics of cis-regulatory contacts upon lineage commitment, including the acquisition and loss of promoter interactions. This spatial rewiring occurs preferentially with predicted changes in the activity of cis-regulatory elements and is associated with changes in target gene expression. Our results provide a global and integrated view of promoter interactome dynamics during lineage commitment of human pluripotent cells.

  9. Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes

    National Research Council Canada - National Science Library

    O'Quin, Kelly E; Smith, Daniel; Naseer, Zan; Schulte, Jane; Engel, Samuel D; Loh, Yong-Hwee E; Streelman, J Todd; Boore, Jeffrey L; Carleton, Karen L

    2011-01-01

    .... We use phylogenetic footprinting and shadowing to examine divergence in conserved non-coding elements, promoter sequences, and 3'-UTRs surrounding each opsin in search of candidate cis-regulatory...

  10. [Role of genes and their cis-regulatory elements during animal morphological evolution].

    Science.gov (United States)

    Sun, Boyuan; Tu, Jianbo; Li, Ying; Yang, Mingyao

    2014-06-01

    Cis-regulatory hypothesis is one of the most important theories in evolutionary developmental biology (evo-devo), which claims that evolution of cis-regulatory elements (CREs) plays a key role during evolution of morphology. However, an increasing number of experimental results show that cis-regulatory hypothesis alone is not far enough to explain the complexity of evo-devo processes. Other modifications, including mutations of protein coding, gene and genome duplications, and flexibility of homeodomains and CREs, also cause the morphological changes in animals. In this review, we retrospect the recent results of evolution of CREs and genes associated with CREs and discuss new methods and trends for research in evo-devo.

  11. A Simple Grammar Defines Activating and Repressing cis-Regulatory Elements in Photoreceptors

    Directory of Open Access Journals (Sweden)

    Michael A. White

    2016-10-01

    Full Text Available Transcription factors often activate and repress different target genes in the same cell. How activation and repression are encoded by different arrangements of transcription factor binding sites in cis-regulatory elements is poorly understood. We investigated how sites for the transcription factor CRX encode both activation and repression in photoreceptors by assaying thousands of genomic and synthetic cis-regulatory elements in wild-type and Crx−/− retinas. We found that sequences with high affinity for CRX repress transcription, whereas sequences with lower affinity activate. This rule is modified by a cooperative interaction between CRX sites and sites for the transcription factor NRL, which overrides the repressive effect of high affinity for CRX. Our results show how simple rearrangements of transcription factor binding sites encode qualitatively different responses to a single transcription factor and explain how CRX plays multiple cis-regulatory roles in the same cell.

  12. Cis-regulatory elements in the primate brain: from functional specialization to neurodegeneration

    NARCIS (Netherlands)

    Vermunt, Marit W.

    2017-01-01

    Over the last decade, the noncoding part of the genome has been shown to harbour thousands of cis-regulatory elements, such as enhancers, that activate well-defined gene expression programs. Here, we charted active enhancers in a multiplicity of human brain regions to understand the role of

  13. Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees

    Directory of Open Access Journals (Sweden)

    Chen Xiaoyu

    2007-12-01

    Full Text Available Abstract Background In vertebrates, a large part of gene transcriptional regulation is operated by cis-regulatory modules. These modules are believed to be regulating much of the tissue-specificity of gene expression. Results We develop a Bayesian network approach for identifying cis-regulatory modules likely to regulate tissue-specific expression. The network integrates predicted transcription factor binding site information, transcription factor expression data, and target gene expression data. At its core is a regression tree modeling the effect of combinations of transcription factors bound to a module. A new unsupervised EM-like algorithm is developed to learn the parameters of the network, including the regression tree structure. Conclusion Our approach is shown to accurately identify known human liver and erythroid-specific modules. When applied to the prediction of tissue-specific modules in 10 different tissues, the network predicts a number of important transcription factor combinations whose concerted binding is associated to specific expression.

  14. Evolved tooth gain in sticklebacks is associated with a cis-regulatory allele of Bmp6.

    Science.gov (United States)

    Cleves, Phillip A; Ellis, Nicholas A; Jimenez, Monica T; Nunez, Stephanie M; Schluter, Dolph; Kingsley, David M; Miller, Craig T

    2014-09-23

    Developmental genetic studies of evolved differences in morphology have led to the hypothesis that cis-regulatory changes often underlie morphological evolution. However, because most of these studies focus on evolved loss of traits, the genetic architecture and possible association with cis-regulatory changes of gain traits are less understood. Here we show that a derived benthic freshwater stickleback population has evolved an approximate twofold gain in ventral pharyngeal tooth number compared with their ancestral marine counterparts. Comparing laboratory-reared developmental time courses of a low-toothed marine population and this high-toothed benthic population reveals that increases in tooth number and tooth plate area and decreases in tooth spacing arise at late juvenile stages. Genome-wide linkage mapping identifies largely separate sets of quantitative trait loci affecting different aspects of dental patterning. One large-effect quantitative trait locus controlling tooth number fine-maps to a genomic region containing an excellent candidate gene, Bone morphogenetic protein 6 (Bmp6). Stickleback Bmp6 is expressed in developing teeth, and no coding changes are found between the high- and low-toothed populations. However, quantitative allele-specific expression assays of Bmp6 in developing teeth in F1 hybrids show that cis-regulatory changes have elevated the relative expression level of the freshwater benthic Bmp6 allele at late, but not early, stages of stickleback development. Collectively, our data support a model where a late-acting cis-regulatory up-regulation of Bmp6 expression underlies a significant increase in tooth number in derived benthic sticklebacks.

  15. Dynamic SPR monitoring of yeast nuclear protein binding to a cis-regulatory element.

    Science.gov (United States)

    Mao, Grace; Brody, James P

    2007-11-09

    Gene expression is controlled by protein complexes binding to short specific sequences of DNA, called cis-regulatory elements. Expression of most eukaryotic genes is controlled by dozens of these elements. Comprehensive identification and monitoring of these elements is a major goal of genomics. In pursuit of this goal, we are developing a surface plasmon resonance (SPR) based assay to identify and monitor cis-regulatory elements. To test whether we could reliably monitor protein binding to a regulatory element, we immobilized a 16bp region of Saccharomyces cerevisiae chromosome 5 onto a gold surface. This 16bp region of DNA is known to bind several proteins and thought to control expression of the gene RNR1, which varies through the cell cycle. We synchronized yeast cell cultures, and then sampled these cultures at a regular interval. These samples were processed to purify nuclear lysate, which was then exposed to the sensor. We found that nuclear protein binds this particular element of DNA at a significantly higher rate (as compared to unsynchronized cells) during G1 phase. Other time points show levels of DNA-nuclear protein binding similar to the unsynchronized control. We also measured the apparent association complex of the binding to be 0.014s(-1). We conclude that (1) SPR-based assays can monitor DNA-nuclear protein binding and that (2) for this particular cis-regulatory element, maximum DNA-nuclear protein binding occurs during G1 phase.

  16. Cis-regulatory Mutations in the Caenorhabditis elegans Homeobox Gene Locus cog-1 Affect Neuronal Development

    Science.gov (United States)

    O'Meara, M. Maggie; Bigelow, Henry; Flibotte, Stephane; Etchberger, John F.; Moerman, Donald G.; Hobert, Oliver

    2009-01-01

    We apply here comparative genome hybridization as a novel tool to identify the molecular lesion in two Caenorhabditis elegans mutant strains that affect a neuronal cell fate decision. The phenotype of the mutant strains resembles those of the loss-of-function alleles of the cog-1 homeobox gene, an inducer of the fate of the gustatory neuron ASER. We find that both lesions map to the cis-regulatory control region of cog-1 and affect a phylogenetically conserved binding site for the C2H2 zinc-finger transcription factor CHE-1, a previously known regulator of cog-1 expression in ASER. Identification of this CHE-1-binding site as a critical regulator of cog-1 expression in the ASER in vivo represents one of the rare demonstrations of the in vivo relevance of an experimentally determined or predicted transcription-factor-binding site. Aside from the mutationally defined CHE-1-binding site, cog-1 contains a second, functional CHE-1-binding site, which in isolation is sufficient to drive reporter gene expression in the ASER but in an in vivo context is apparently insufficient for promoting appropriate ASER expression. The cis-regulatory control regions of other ASE-expressed genes also contain ASE motifs that can promote ASE neuron expression when isolated from their genomic context, but appear to depend on multiple ASE motifs in their normal genomic context. The multiplicity of cis-regulatory elements may ensure the robustness of gene expression. PMID:19189954

  17. The identification of cis-regulatory elements: A review from a machine learning perspective.

    Science.gov (United States)

    Li, Yifeng; Chen, Chih-Yu; Kaye, Alice M; Wasserman, Wyeth W

    2015-12-01

    The majority of the human genome consists of non-coding regions that have been called junk DNA. However, recent studies have unveiled that these regions contain cis-regulatory elements, such as promoters, enhancers, silencers, insulators, etc. These regulatory elements can play crucial roles in controlling gene expressions in specific cell types, conditions, and developmental stages. Disruption to these regions could contribute to phenotype changes. Precisely identifying regulatory elements is key to deciphering the mechanisms underlying transcriptional regulation. Cis-regulatory events are complex processes that involve chromatin accessibility, transcription factor binding, DNA methylation, histone modifications, and the interactions between them. The development of next-generation sequencing techniques has allowed us to capture these genomic features in depth. Applied analysis of genome sequences for clinical genetics has increased the urgency for detecting these regions. However, the complexity of cis-regulatory events and the deluge of sequencing data require accurate and efficient computational approaches, in particular, machine learning techniques. In this review, we describe machine learning approaches for predicting transcription factor binding sites, enhancers, and promoters, primarily driven by next-generation sequencing data. Data sources are provided in order to facilitate testing of novel methods. The purpose of this review is to attract computational experts and data scientists to advance this field.

  18. Bounded search for de novo identification of degenerate cis-regulatory elements

    Directory of Open Access Journals (Sweden)

    Khetani Radhika S

    2006-05-01

    Full Text Available Abstract Background The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-counting strategy for their identification. While numerous methods exist for inferring base distributions using a position weight matrix, recent studies suggest that the independence assumptions inherent in the model, as well as the inability to reach a global optimum, limit this approach. Results In this paper, we report PRISM, a degenerate motif finder that leverages the relationship between the statistical significance of a set of binding sites and that of the individual binding sites. PRISM first identifies overrepresented, non-degenerate consensus motifs, then iteratively relaxes each one into a high-scoring degenerate motif. This approach requires no tunable parameters, thereby lending itself to unbiased performance comparisons. We therefore compare PRISM's performance against nine popular motif finders on 28 well-characterized S. cerevisiae regulons. PRISM consistently outperforms all other programs. Finally, we use PRISM to predict the binding sites of uncharacterized regulons. Our results support a proposed mechanism of action for the yeast cell-cycle transcription factor Stb1, whose binding site has not been determined experimentally. Conclusion The relationship between statistical measures of the binding sites and the set as a whole leads to a simple means of identifying the diverse range of cis-regulatory elements to which a protein binds. This approach leverages the advantages of word-counting, in that position dependencies are implicitly accounted for and local optima are more easily avoided. While we sacrifice guaranteed optimality to prevent the exponential blowup of exhaustive search, we prove that the error

  19. Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells.

    Directory of Open Access Journals (Sweden)

    Anthony A Philippakis

    2006-05-01

    Full Text Available While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need for computational methods that can evaluate hypothesized cis regulatory codes before the difficult task of experimental verification is undertaken. We have developed a novel computational framework (termed "CodeFinder" that integrates transcription factor binding site and gene expression information to evaluate whether a hypothesized transcriptional regulatory model (TRM; i.e., a set of co-regulating transcription factors is likely to target a given set of co-expressed genes. Our basic approach is to simultaneously predict cis regulatory modules (CRMs associated with a given gene set and quantify the enrichment for combinatorial subsets of transcription factor binding site motifs comprising the hypothesized TRM within these predicted CRMs. As a model system, we have examined a TRM experimentally demonstrated to drive the expression of two genes in a sub-population of cells in the developing Drosophila mesoderm, the somatic muscle founder cells. This TRM was previously hypothesized to be a general mode of regulation for genes expressed in this cell population. In contrast, the present analyses suggest that a modified form of this cis regulatory code applies to only a subset of founder cell genes, those whose gene expression responds to specific genetic perturbations in a similar manner to the gene on which the original model was based. We have confirmed this hypothesis by experimentally discovering six (out of 12 tested new CRMs driving expression in the embryonic mesoderm, four of which drive expression in founder cells.

  20. Are Interactions between cis-Regulatory Variants Evidence for Biological Epistasis or Statistical Artifacts?

    Science.gov (United States)

    Fish, Alexandra E; Capra, John A; Bush, William S

    2016-10-06

    The importance of epistasis-or statistical interactions between genetic variants-to the development of complex disease in humans has been controversial. Genome-wide association studies of statistical interactions influencing human traits have recently become computationally feasible and have identified many putative interactions. However, statistical models used to detect interactions can be confounded, which makes it difficult to be certain that observed statistical interactions are evidence for true molecular epistasis. In this study, we investigate whether there is evidence for epistatic interactions between genetic variants within the cis-regulatory region that influence gene expression after accounting for technical, statistical, and biological confounding factors. We identified 1,119 (FDR = 5%) interactions that appear to regulate gene expression in human lymphoblastoid cell lines, a tightly controlled, largely genetically determined phenotype. Many of these interactions replicated in an independent dataset (90 of 803 tested, Bonferroni threshold). We then performed an exhaustive analysis of both known and novel confounders, including ceiling/floor effects, missing genotype combinations, haplotype effects, single variants tagged through linkage disequilibrium, and population stratification. Every interaction could be explained by at least one of these confounders, and replication in independent datasets did not protect against some confounders. Assuming that the confounding factors provide a more parsimonious explanation for each interaction, we find it unlikely that cis-regulatory interactions contribute strongly to human gene expression, which calls into question the relevance of cis-regulatory interactions for other human phenotypes. We additionally propose several best practices for epistasis testing to protect future studies from confounding. Copyright © 2016 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  1. On the Concept of Cis-regulatory Information: From Sequence Motifs to Logic Functions

    Science.gov (United States)

    Tarpine, Ryan; Istrail, Sorin

    The regulatory genome is about the “system level organization of the core genomic regulatory apparatus, and how this is the locus of causality underlying the twin phenomena of animal development and animal evolution” (E.H. Davidson. The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, Academic Press, 2006). Information processing in the regulatory genome is done through regulatory states, defined as sets of transcription factors (sequence-specific DNA binding proteins which determine gene expression) that are expressed and active at the same time. The core information processing machinery consists of modular DNA sequence elements, called cis-modules, that interact with transcription factors. The cis-modules “read” the information contained in the regulatory state of the cell through transcription factor binding, “process” it, and directly or indirectly communicate with the basal transcription apparatus to determine gene expression. This endowment of each gene with the information-receiving capacity through their cis-regulatory modules is essential for the response to every possible regulatory state to which it might be exposed during all phases of the life cycle and in all cell types. We present here a set of challenges addressed by our CYRENE research project aimed at studying the cis-regulatory code of the regulatory genome. The CYRENE Project is devoted to (1) the construction of a database, the cis-Lexicon, containing comprehensive information across species about experimentally validated cis-regulatory modules; and (2) the software development of a next-generation genome browser, the cis-Browser, specialized for the regulatory genome. The presentation is anchored on three main computational challenges: the Gene Naming Problem, the Consensus Sequence Bottleneck Problem, and the Logic Function Inference Problem.

  2. Rapid evolution of cis-regulatory sequences via local point mutations

    Science.gov (United States)

    Stone, J. R.; Wray, G. A.

    2001-01-01

    Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.

  3. Identification of a cis-regulatory element by transient analysis of co-ordinately regulated genes

    Directory of Open Access Journals (Sweden)

    Allan Andrew C

    2008-07-01

    Full Text Available Abstract Background Transcription factors (TFs co-ordinately regulate target genes that are dispersed throughout the genome. This co-ordinate regulation is achieved, in part, through the interaction of transcription factors with conserved cis-regulatory motifs that are in close proximity to the target genes. While much is known about the families of transcription factors that regulate gene expression in plants, there are few well characterised cis-regulatory motifs. In Arabidopsis, over-expression of the MYB transcription factor PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT 1 leads to transgenic plants with elevated anthocyanin levels due to the co-ordinated up-regulation of genes in the anthocyanin biosynthetic pathway. In addition to the anthocyanin biosynthetic genes, there are a number of un-associated genes that also change in expression level. This may be a direct or indirect consequence of the over-expression of PAP1. Results Oligo array analysis of PAP1 over-expression Arabidopsis plants identified genes co-ordinately up-regulated in response to the elevated expression of this transcription factor. Transient assays on the promoter regions of 33 of these up-regulated genes identified eight promoter fragments that were transactivated by PAP1. Bioinformatic analysis on these promoters revealed a common cis-regulatory motif that we showed is required for PAP1 dependent transactivation. Conclusion Co-ordinated gene regulation by individual transcription factors is a complex collection of both direct and indirect effects. Transient transactivation assays provide a rapid method to identify direct target genes from indirect target genes. Bioinformatic analysis of the promoters of these direct target genes is able to locate motifs that are common to this sub-set of promoters, which is impossible to identify with the larger set of direct and indirect target genes. While this type of analysis does not prove a direct interaction between protein and DNA

  4. Identification of Distal cis-Regulatory Elements at Mouse Mitoferrin Loci Using Zebrafish Transgenesis▿

    OpenAIRE

    Amigo, J. D.; Yu, M.; Troadec, M.-B.; Gwynn, B; Cooney, J. D.; Lambert, A.J.; Chi, N. C.; Weiss, M J; Peters, L. L.; Kaplan, J; Cantor, Alan B.; Paw, Barry Htin

    2011-01-01

    Mitoferrin 1 (Mfrn1; Slc25a37) and mitoferrin 2 (Mfrn2; Slc25a28) function as essential mitochondrial iron importers for heme and Fe/S cluster biogenesis. A genetic deficiency of Mfrn1 results in a profound hypochromic anemia in vertebrate species. To map the cis-regulatory modules (CRMs) that control expression of the Mfrn genes, we utilized genome-wide chromatin immunoprecipitation (ChIP) datasets for the major erythroid transcription factor GATA-1. We identified the CRMs that faithfully dr...

  5. Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes

    Directory of Open Access Journals (Sweden)

    Streelman J Todd

    2011-05-01

    Full Text Available Abstract Background Divergence within cis-regulatory sequences may contribute to the adaptive evolution of gene expression, but functional alleles in these regions are difficult to identify without abundant genomic resources. Among African cichlid fishes, the differential expression of seven opsin genes has produced adaptive differences in visual sensitivity. Quantitative genetic analysis suggests that cis-regulatory alleles near the SWS2-LWS opsins may contribute to this variation. Here, we sequence BACs containing the opsin genes of two cichlids, Oreochromis niloticus and Metriaclima zebra. We use phylogenetic footprinting and shadowing to examine divergence in conserved non-coding elements, promoter sequences, and 3'-UTRs surrounding each opsin in search of candidate cis-regulatory sequences that influence cichlid opsin expression. Results We identified 20 conserved non-coding elements surrounding the opsins of cichlids and other teleosts, including one known enhancer and a retinal microRNA. Most conserved elements contained computationally-predicted binding sites that correspond to transcription factors that function in vertebrate opsin expression; O. niloticus and M. zebra were significantly divergent in two of these. Similarly, we found a large number of relevant transcription factor binding sites within each opsin's proximal promoter, and identified five opsins that were considerably divergent in both expression and the number of transcription factor binding sites shared between O. niloticus and M. zebra. We also found several microRNA target sites within the 3'-UTR of each opsin, including two 3'-UTRs that differ significantly between O. niloticus and M. zebra. Finally, we examined interspecific divergence among 18 phenotypically diverse cichlids from Lake Malawi for one conserved non-coding element, two 3'-UTRs, and five opsin proximal promoters. We found that all regions were highly conserved with some evidence of CRX transcription

  6. Engineering Synthetic cis-Regulatory Elements for Simultaneous Recognition of Three Transcriptional Factors in Bacteria.

    Science.gov (United States)

    Amores, Gerardo Ruiz; Guazzaroni, María-Eugenia; Silva-Rocha, Rafael

    2015-12-18

    Recognition of cis-regulatory elements by transcription factors (TF) at target promoters is crucial to gene regulation in bacteria. In this process, binding of TFs to their cognate sequences depends on a set of physical interactions between these proteins and specific nucleotides in the operator region. Previously, we showed that in silico optimization algorithms are able to generate short sequences that are recognized by two different TFs of Escherichia coli, namely, CRP and IHF, thus generating an AND logic gate. Here, we expanded this approach in order to engineer DNA sequences that can be simultaneously recognized by three unrelated TFs (CRP, IHF, and Fis). Using in silico optimization and experimental validation strategies, we were able to obtain a candidate promoter (Plac-CFI1) regulated by only two TFs with an AND logic, thus demonstrating a limitation in the design. Subsequently, we modified the algorithm to allow the optimization of extended sequences, and were able to design two synthetic promoters (PCFI20-1 and PCFI22-5) that were functional in vivo. Expression assays in E. coli mutant strains for each TF revealed that while CRP positively regulates the promoter activities, IHF and Fis are strong repressors of both the promoter variants. Taken together, our results demonstrate the potential of in silico strategies in bacterial synthetic promoter engineering. Furthermore, the study also shows how small modifications in cis-regulatory elements can drastically affect the final logic of the resulting promoter.

  7. Dissection of cis-regulatory elements in the C. elegans Hox gene egl-5 promoter.

    Science.gov (United States)

    Teng, Yingqi; Girard, Lisa; Ferreira, Henrique B; Sternberg, Paul W; Emmons, Scott W

    2004-12-15

    Hox genes are highly conserved segmental identity genes well known for their complex expression patterns and divergent targets. Here we present an analysis of cis-regulatory elements in the Caenorhabditis elegans Hox gene egl-5, which is expressed in multiple tissues in the posterior region of the nematode. We have utilized phylogenetic footprinting to efficiently identify cis-regulatory elements and have characterized these with gfp reporters and tissue-specific rescue experiments. We have found that the complex expression pattern of egl-5 is the cumulative result of the activities of multiple tissue or local region-specific activator sequences that are conserved both in sequence and near-perfect order in the related nematode Caenorhabditis briggsae. Two conserved regulatory blocks analyzed in detail contain multiple sites for both positively and negatively acting factors. One of these regions may promote activation of egl-5 in certain cells via the Wnt pathway. Positively acting regions are repressed in inappropriate tissues by additional negative pathways acting at other sites within the promoter. Our analysis has allowed us to implicate several new regulatory factors significant to the control of egl-5 expression.

  8. Plasticity of the cis-regulatory input function of a gene.

    Directory of Open Access Journals (Sweden)

    Avraham E Mayo

    2006-04-01

    Full Text Available The transcription rate of a gene is often controlled by several regulators that bind specific sites in the gene's cis-regulatory region. The combined effect of these regulators is described by a cis-regulatory input function. What determines the form of an input function, and how variable is it with respect to mutations? To address this, we employ the well-characterized lac operon of Escherichia coli, which has an elaborate input function, intermediate between Boolean AND-gate and OR-gate logic. We mapped in detail the input function of 12 variants of the lac promoter, each with different point mutations in the regulator binding sites, by means of accurate expression measurements from living cells. We find that even a few mutations can significantly change the input function, resulting in functions that resemble Pure AND gates, OR gates, or single-input switches. Other types of gates were not found. The variant input functions can be described in a unified manner by a mathematical model. The model also lets us predict which functions cannot be reached by point mutations. The input function that we studied thus appears to be plastic, in the sense that many of the mutations do not ruin the regulation completely but rather result in new ways to integrate the inputs.

  9. The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron

    Science.gov (United States)

    Etchberger, John F.; Lorch, Adam; Sleumer, Monica C.; Zapf, Richard; Jones, Steven J.; Marra, Marco A.; Holt, Robert A.; Moerman, Donald G.; Hobert, Oliver

    2007-01-01

    Taste receptor cells constitute a highly specialized cell type that perceives and conveys specific sensory information to the brain. The detailed molecular composition of these cells and the mechanisms that program their fate are, in general, poorly understood. We have generated serial analysis of gene expression (SAGE) libraries from two distinct populations of single, isolated sensory neuron classes, the gustatory neuron class ASE and the thermosensory neuron class AFD, from the nematode Caenorhabditis elegans. By comparing these two libraries, we have identified >1000 genes that define the ASE gustatory neuron class on a molecular level. This set of genes contains determinants of the differentiated state of the ASE neuron, such as a surprisingly complex repertoire of transcription factors (TFs), ion channels, neurotransmitters, and receptors, as well as seven-transmembrane receptor (7TMR)-type putative gustatory receptor genes. Through the in vivo dissection of the cis-regulatory regions of several ASE-expressed genes, we identified a small cis-regulatory motif, the “ASE motif,” that is required for the expression of many ASE-expressed genes. We demonstrate that the ASE motif is a binding site for the C2H2 zinc finger TF CHE-1, which is essential for the correct differentiation of the ASE gustatory neuron. Taken together, our results provide a unique view of the molecular landscape of a single neuron type and reveal an important aspect of the regulatory logic for gustatory neuron specification in C. elegans. PMID:17606643

  10. Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis.

    Directory of Open Access Journals (Sweden)

    Michalis Barkoulas

    2016-09-01

    Full Text Available Patterning of C. elegans vulval cell fates relies on inductive signaling. In this induction event, a single cell, the gonadal anchor cell, secretes LIN-3/EGF and induces three out of six competent precursor cells to acquire a vulval fate. We previously showed that this developmental system is robust to a four-fold variation in lin-3/EGF genetic dose. Here using single-molecule FISH, we find that the mean level of expression of lin-3 in the anchor cell is remarkably conserved. No change in lin-3 expression level could be detected among C. elegans wild isolates and only a low level of change-less than 30%-in the Caenorhabditis genus and in Oscheius tipulae. In C. elegans, lin-3 expression in the anchor cell is known to require three transcription factor binding sites, specifically two E-boxes and a nuclear-hormone-receptor (NHR binding site. Mutation of any of these three elements in C. elegans results in a dramatic decrease in lin-3 expression. Yet only a single E-box is found in the Drosophilae supergroup of Caenorhabditis species, including C. angaria, while the NHR-binding site likely only evolved at the base of the Elegans group. We find that a transgene from C. angaria bearing a single E-box is sufficient for normal expression in C. elegans. Even a short 58 bp cis-regulatory fragment from C. angaria with this single E-box is able to replace the three transcription factor binding sites at the endogenous C. elegans lin-3 locus, resulting in the wild-type expression level. Thus, regulatory evolution occurring in cis within a 58 bp lin-3 fragment, results in a strict requirement for the NHR binding site and a second E-box in C. elegans. This single-cell, single-molecule, quantitative and functional evo-devo study demonstrates that conserved expression levels can hide extensive change in cis-regulatory site requirements and highlights the evolution of new cis-regulatory elements required for cell-specific gene expression.

  11. Lessons from Domestication: Targeting Cis-Regulatory Elements for Crop Improvement.

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    Swinnen, Gwen; Goossens, Alain; Pauwels, Laurens

    2016-06-01

    Domestication of wild plant species has provided us with crops that serve our human nutritional needs. Advanced DNA sequencing has propelled the unveiling of underlying genetic changes associated with domestication. Interestingly, many changes reside in cis-regulatory elements (CREs) that control the expression of an unmodified coding sequence. Sequence variation in CREs can impact gene expression levels, but also developmental timing and tissue specificity of expression. When genes are involved in multiple pathways or active in several organs and developmental stages CRE modifications are favored in contrast to mutations in coding regions, due to the lack of detrimental pleiotropic effects. Therefore, learning from domestication, we propose that CREs are interesting targets for genome editing to create new alleles for plant breeding.

  12. Establishment of the methods for searching eukaryotic gene cis-regulatory modules.

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    Zhong, Dong; Zhang, Zhen-shu; Liu, Yu-hu; Zheng, Guo-qing; Liu, Xiao-yi; Lu, Yang; Zhao, Gui-jun; Xu, An-long

    2004-02-01

    On the basis of the knowledge of eukaryotic gene regulation, we modified the method in three aspects: (1) Searching the cis-regulatory modules (CRM) according Fasta or Blast sequence with multiple sequence and low E value, followed by mutual scoring of these sequence with Smith-Waterman algorithms and finally by clustering analysis; (2) Searching the transcription factor-binding site using International Union of Pure and Applied Chemistry, Position-Weight Matrix(PWM) and Dyed method; (3) Designing and implementation of data analysis based on the software in Windows 2000 and UNIX using object-oriented technology. The results of analysis of the major histocompatibility complex gene family show that this procedure may accurately locate the regions that contain some of the CRMs.

  13. Massively parallel cis-regulatory analysis in the mammalian central nervous system.

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    Shen, Susan Q; Myers, Connie A; Hughes, Andrew E O; Byrne, Leah C; Flannery, John G; Corbo, Joseph C

    2016-02-01

    Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies in functionally interpreting these data. To address this issue, massively parallel reporter assays (MPRAs) have emerged, in which barcoded reporter libraries are introduced into cells, and the resulting barcoded transcripts are quantified by next-generation sequencing. Thus far, MPRAs have been largely restricted to assaying short CREs in a limited repertoire of cultured cell types. Here, we present two advances that extend the biological relevance and applicability of MPRAs. First, we adapt exome capture technology to instead capture candidate CREs, thereby tiling across the targeted regions and markedly increasing the length of CREs that can be readily assayed. Second, we package the library into adeno-associated virus (AAV), thereby allowing delivery to target organs in vivo. As a proof of concept, we introduce a capture library of about 46,000 constructs, corresponding to roughly 3500 DNase I hypersensitive (DHS) sites, into the mouse retina by ex vivo plasmid electroporation and into the mouse cerebral cortex by in vivo AAV injection. We demonstrate tissue-specific cis-regulatory activity of DHSs and provide examples of high-resolution truncation mutation analysis for multiplex parsing of CREs. Our approach should enable massively parallel functional analysis of a wide range of CREs in any organ or species that can be infected by AAV, such as nonhuman primates and human stem cell-derived organoids.

  14. Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4.

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    Hanikenne, Marc; Talke, Ina N; Haydon, Michael J; Lanz, Christa; Nolte, Andrea; Motte, Patrick; Kroymann, Juergen; Weigel, Detlef; Krämer, Ute

    2008-05-15

    Little is known about the types of mutations underlying the evolution of species-specific traits. The metal hyperaccumulator Arabidopsis halleri has the rare ability to colonize heavy-metal-polluted soils, and, as an extremophile sister species of Arabidopsis thaliana, it is a powerful model for research on adaptation. A. halleri naturally accumulates and tolerates leaf concentrations as high as 2.2% zinc and 0.28% cadmium in dry biomass. On the basis of transcriptomics studies, metal hyperaccumulation in A. halleri has been associated with more than 30 candidate genes that are expressed at higher levels in A. halleri than in A. thaliana. Some of these genes have been genetically mapped to broad chromosomal segments of between 4 and 24 cM co-segregating with Zn and Cd hypertolerance. However, the in planta loss-of-function approaches required to demonstrate the contribution of a given candidate gene to metal hyperaccumulation or hypertolerance have not been pursued to date. Using RNA interference to downregulate HMA4 (HEAVY METAL ATPASE 4) expression, we show here that Zn hyperaccumulation and full hypertolerance to Cd and Zn in A. halleri depend on the metal pump HMA4. Contrary to a postulated global trans regulatory factor governing high expression of numerous metal hyperaccumulation genes, we demonstrate that enhanced expression of HMA4 in A. halleri is attributable to a combination of modified cis-regulatory sequences and copy number expansion, in comparison to A. thaliana. Transfer of an A. halleri HMA4 gene to A. thaliana recapitulates Zn partitioning into xylem vessels and the constitutive transcriptional upregulation of Zn deficiency response genes characteristic of Zn hyperaccumulators. Our results demonstrate the importance of cis-regulatory mutations and gene copy number expansion in the evolution of a complex naturally selected extreme trait. The elucidation of a natural strategy for metal hyperaccumulation enables the rational design of technologies

  15. Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.

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    Diana S José-Edwards

    2015-12-01

    Full Text Available A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chordates. Although numerous notochord genes have been identified, the regulatory DNAs that orchestrate development and propel evolution of this structure by eliciting notochord gene expression remain mostly uncharted, and the information on their configuration and recurrence is still quite fragmentary. Here we used the simple chordate Ciona for a systematic analysis of notochord cis-regulatory modules (CRMs, and investigated their composition, architectural constraints, predictive ability and evolutionary conservation. We found that most Ciona notochord CRMs relied upon variable combinations of binding sites for the transcription factors Brachyury and/or Foxa2, which can act either synergistically or independently from one another. Notably, one of these CRMs contains a Brachyury binding site juxtaposed to an (AC microsatellite, an unusual arrangement also found in Brachyury-bound regulatory regions in mouse. In contrast, different subsets of CRMs relied upon binding sites for transcription factors of widely diverse families. Surprisingly, we found that neither intra-genomic nor interspecific conservation of binding sites were reliably predictive hallmarks of notochord CRMs. We propose that rather than obeying a rigid sequence-based cis-regulatory code, most notochord CRMs are rather unique. Yet, this study uncovered essential elements recurrently used by divergent chordates as basic building blocks for notochord CRMs.

  16. Identification of putative cis-regulatory elements in Cryptosporidium parvum by de novo pattern finding

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    Kissinger Jessica C

    2007-01-01

    Full Text Available Abstract Background Cryptosporidium parvum is a unicellular eukaryote in the phylum Apicomplexa. It is an obligate intracellular parasite that causes diarrhea and is a significant AIDS-related pathogen. Cryptosporidium parvum is not amenable to long-term laboratory cultivation or classical molecular genetic analysis. The parasite exhibits a complex life cycle, a broad host range, and fundamental mechanisms of gene regulation remain unknown. We have used data from the recently sequenced genome of this organism to uncover clues about gene regulation in C. parvum. We have applied two pattern finding algorithms MEME and AlignACE to identify conserved, over-represented motifs in the 5' upstream regions of genes in C. parvum. To support our findings, we have established comparative real-time -PCR expression profiles for the groups of genes examined computationally. Results We find that groups of genes that share a function or belong to a common pathway share upstream motifs. Different motifs are conserved upstream of different groups of genes. Comparative real-time PCR studies show co-expression of genes within each group (in sub-sets during the life cycle of the parasite, suggesting co-regulation of these genes may be driven by the use of conserved upstream motifs. Conclusion This is one of the first attempts to characterize cis-regulatory elements in the absence of any previously characterized elements and with very limited expression data (seven genes only. Using de novo pattern finding algorithms, we have identified specific DNA motifs that are conserved upstream of genes belonging to the same metabolic pathway or gene family. We have demonstrated the co-expression of these genes (often in subsets using comparative real-time-PCR experiments thus establishing evidence for these conserved motifs as putative cis-regulatory elements. Given the lack of prior information concerning expression patterns and organization of promoters in C. parvum we

  17. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

    Science.gov (United States)

    He, Xin; Ling, Xu; Sinha, Saurabh

    2009-03-01

    Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs) and understanding their evolution. The comparison requires reliable sequence alignment, which remains a challenging task for less conserved noncoding sequences. Furthermore, the existing models of DNA sequence evolution generally do not explicitly treat the special properties of CRM sequences. To address these limitations, we propose a model of CRM evolution that captures different modes of evolution of functional transcription factor binding sites (TFBSs) and the background sequences. A particularly novel aspect of our work is a probabilistic model of gains and losses of TFBSs, a process being recognized as an important part of regulatory sequence evolution. We present a computational framework that uses this model to solve the problems of CRM alignment and prediction. Our alignment method is similar to existing methods of statistical alignment but uses the conserved binding sites to improve alignment. Our CRM prediction method deals with the inherent uncertainties of binding site annotations and sequence alignment in a probabilistic framework. In simulated as well as real data, we demonstrate that our program is able to improve both alignment and prediction of CRM sequences over several state-of-the-art methods. Finally, we used alignments produced by our program to study binding site conservation in genome-wide binding data of key transcription factors in the Drosophila blastoderm, with two intriguing results: (i) the factor-bound sequences are under strong evolutionary constraints even if their neighboring genes are not expressed in the blastoderm and (ii) binding sites in distal bound sequences (relative to transcription start sites) tend to be more conserved than those in proximal regions. Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis), ready to be applied in a broad biological context.

  18. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

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    Xin He

    2009-03-01

    Full Text Available Cross-species comparison has emerged as a powerful paradigm for predicting cis-regulatory modules (CRMs and understanding their evolution. The comparison requires reliable sequence alignment, which remains a challenging task for less conserved noncoding sequences. Furthermore, the existing models of DNA sequence evolution generally do not explicitly treat the special properties of CRM sequences. To address these limitations, we propose a model of CRM evolution that captures different modes of evolution of functional transcription factor binding sites (TFBSs and the background sequences. A particularly novel aspect of our work is a probabilistic model of gains and losses of TFBSs, a process being recognized as an important part of regulatory sequence evolution. We present a computational framework that uses this model to solve the problems of CRM alignment and prediction. Our alignment method is similar to existing methods of statistical alignment but uses the conserved binding sites to improve alignment. Our CRM prediction method deals with the inherent uncertainties of binding site annotations and sequence alignment in a probabilistic framework. In simulated as well as real data, we demonstrate that our program is able to improve both alignment and prediction of CRM sequences over several state-of-the-art methods. Finally, we used alignments produced by our program to study binding site conservation in genome-wide binding data of key transcription factors in the Drosophila blastoderm, with two intriguing results: (i the factor-bound sequences are under strong evolutionary constraints even if their neighboring genes are not expressed in the blastoderm and (ii binding sites in distal bound sequences (relative to transcription start sites tend to be more conserved than those in proximal regions. Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis, ready to be applied in a broad biological context.

  19. In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression.

    Science.gov (United States)

    Zagrijchuk, Elizaveta A; Sabirov, Marat A; Holloway, David M; Spirov, Alexander V

    2014-04-01

    Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes.

  20. Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence.

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    Dara G Torgerson

    2009-08-01

    Full Text Available Analysis of polymorphism and divergence in the non-coding portion of the human genome yields crucial information about factors driving the evolution of gene regulation. Candidate cis-regulatory regions spanning more than 15,000 genes in 15 African Americans and 20 European Americans were re-sequenced and aligned to the chimpanzee genome in order to identify potentially functional polymorphism and to characterize and quantify departures from neutral evolution. Distortions of the site frequency spectra suggest a general pattern of selective constraint on conserved non-coding sites in the flanking regions of genes (CNCs. Moreover, there is an excess of fixed differences that cannot be explained by a Gamma model of deleterious fitness effects, suggesting the presence of positive selection on CNCs. Extensions of the McDonald-Kreitman test identified candidate cis-regulatory regions with high probabilities of positive and negative selection near many known human genes, the biological characteristics of which exhibit genome-wide trends that differ from patterns observed in protein-coding regions. Notably, there is a higher probability of positive selection in candidate cis-regulatory regions near genes expressed in the fetal brain, suggesting that a larger portion of adaptive regulatory changes has occurred in genes expressed during brain development. Overall we find that natural selection has played an important role in the evolution of candidate cis-regulatory regions throughout hominid evolution.

  1. Prediction of Cis-Regulatory Elements Controlling Genes Differentially Expressed by Retinal and Choroidal Vascular Endothelial Cells.

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    Choi, Dongseok; Appukuttan, Binoy; Binek, Sierra J; Planck, Stephen R; Stout, J Timothy; Rosenbaum, James T; Smith, Justine R

    2008-01-01

    Cultured endothelial cells of the human retina and choroid demonstrate distinct patterns of gene expression. We hypothesized that differential gene expression reflected differences in the interactions of transcription factors and respective cis-regulatory motifs(s) in these two emdothelial cell subpopulations, recognizing that motifs often exist as modules. We tested this hypothesis in silico by using TRANSFAC Professional and CisModule to identify cis-regulatory motifs and modules in genes that were differentially expressed by human retinal versus choroidal endothelial cells, as identified by analysis of a microarray data set. Motifs corresponding to eight transcription factors were significantly (p < 0.05) differentially abundant in genes that were relatively highly expressed in retinal (i.e., GCCR, HMGIY, HSF1, p53, VDR) or choroidal (i.e., E2F, YY1, ZF5) endothelial cells. Predicted cis-regulatory modules were quite different for these two groups of genes. Our findings raise the possibility of exploiting specific cis-regulatory motifs to target therapy at the ocular endothelial cells subtypes responsible for neovascular age-related macular degeneration or proliferative diabetic retinopathy.

  2. cis-Regulatory control of the initial neurogenic pattern of onecut gene expression in the sea urchin embryo.

    Science.gov (United States)

    Barsi, Julius C; Davidson, Eric H

    2016-01-01

    Specification of the ciliated band (CB) of echinoid embryos executes three spatial functions essential for postgastrular organization. These are establishment of a band about 5 cells wide which delimits and bounds other embryonic territories; definition of a neurogenic domain within this band; and generation within it of arrays of ciliary cells that bear the special long cilia from which the structure derives its name. In Strongylocentrotus purpuratus the spatial coordinates of the future ciliated band are initially and exactly determined by the disposition of a ring of cells that transcriptionally activate the onecut homeodomain regulatory gene, beginning in blastula stage, long before the appearance of the CB per se. Thus the cis-regulatory apparatus that governs onecut expression in the blastula directly reveals the genomic sequence code by which these aspects of the spatial organization of the embryo are initially determined. We screened the entire onecut locus and its flanking region for transcriptionally active cis-regulatory elements, and by means of BAC recombineered deletions identified three separated and required cis-regulatory modules that execute different functions. The operating logic of the crucial spatial control module accounting for the spectacularly precise and beautiful early onecut expression domain depends on spatial repression. Previously predicted oral ectoderm and aboral ectoderm repressors were identified by cis-regulatory mutation as the products of goosecoid and irxa genes respectively, while the pan-ectodermal activator SoxB1 supplies a transcriptional driver function.

  3. In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression

    Science.gov (United States)

    Zagrijchuk, Elizaveta A.; Sabirov, Marat A.; Holloway, David M.; Spirov, Alexander V.

    2014-01-01

    Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes. PMID:24712536

  4. Distinct functional constraints partition sequence conservation in a cis-regulatory element.

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    Antoine Barrière

    2011-06-01

    Full Text Available Different functional constraints contribute to different evolutionary rates across genomes. To understand why some sequences evolve faster than others in a single cis-regulatory locus, we investigated function and evolutionary dynamics of the promoter of the Caenorhabditis elegans unc-47 gene. We found that this promoter consists of two distinct domains. The proximal promoter is conserved and is largely sufficient to direct appropriate spatial expression. The distal promoter displays little if any conservation between several closely related nematodes. Despite this divergence, sequences from all species confer robustness of expression, arguing that this function does not require substantial sequence conservation. We showed that even unrelated sequences have the ability to promote robust expression. A prominent feature shared by all of these robustness-promoting sequences is an AT-enriched nucleotide composition consistent with nucleosome depletion. Because general sequence composition can be maintained despite sequence turnover, our results explain how different functional constraints can lead to vastly disparate rates of sequence divergence within a promoter.

  5. Characterization of Putative cis-Regulatory Elements in Genes Preferentially Expressed in Arabidopsis Male Meiocytes

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    Junhua Li

    2014-01-01

    Full Text Available Meiosis is essential for plant reproduction because it is the process during which homologous chromosome pairing, synapsis, and meiotic recombination occur. The meiotic transcriptome is difficult to investigate because of the size of meiocytes and the confines of anther lobes. The recent development of isolation techniques has enabled the characterization of transcriptional profiles in male meiocytes of Arabidopsis. Gene expression in male meiocytes shows unique features. The direct interaction of transcription factors (TFs with DNA regulatory sequences forms the basis for the specificity of transcriptional regulation. Here, we identified putative cis-regulatory elements (CREs associated with male meiocyte-expressed genes using in silico tools. The upstream regions (1 kb of the top 50 genes preferentially expressed in Arabidopsis meiocytes possessed conserved motifs. These motifs are putative binding sites of TFs, some of which share common functions, such as roles in cell division. In combination with cell-type-specific analysis, our findings could be a substantial aid for the identification and experimental verification of the protein-DNA interactions for the specific TFs that drive gene expression in meiocytes.

  6. Identification of distal cis-regulatory elements at mouse mitoferrin loci using zebrafish transgenesis.

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    Amigo, Julio D; Yu, Ming; Troadec, Marie-Berengere; Gwynn, Babette; Cooney, Jeffrey D; Lambert, Amy J; Chi, Neil C; Weiss, Mitchell J; Peters, Luanne L; Kaplan, Jerry; Cantor, Alan B; Paw, Barry H

    2011-04-01

    Mitoferrin 1 (Mfrn1; Slc25a37) and mitoferrin 2 (Mfrn2; Slc25a28) function as essential mitochondrial iron importers for heme and Fe/S cluster biogenesis. A genetic deficiency of Mfrn1 results in a profound hypochromic anemia in vertebrate species. To map the cis-regulatory modules (CRMs) that control expression of the Mfrn genes, we utilized genome-wide chromatin immunoprecipitation (ChIP) datasets for the major erythroid transcription factor GATA-1. We identified the CRMs that faithfully drive the expression of Mfrn1 during blood and heart development and Mfrn2 ubiquitously. Through in vivo analyses of the Mfrn-CRMs in zebrafish and mouse, we demonstrate their functional and evolutionary conservation. Using knockdowns with morpholinos and cell sorting analysis in transgenic zebrafish embryos, we show that GATA-1 directly regulates the expression of Mfrn1. Mutagenesis of individual GATA-1 binding cis elements (GBE) demonstrated that at least two of the three GBE within this CRM are functionally required for GATA-mediated transcription of Mfrn1. Furthermore, ChIP assays demonstrate switching from GATA-2 to GATA-1 at these elements during erythroid maturation. Our results provide new insights into the genetic regulation of mitochondrial function and iron homeostasis and, more generally, illustrate the utility of genome-wide ChIP analysis combined with zebrafish transgenesis for identifying long-range transcriptional enhancers that regulate tissue development.

  7. Understanding the Dynamics of Gene Regulatory Systems; Characterisation and Clinical Relevance of cis-Regulatory Polymorphisms

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    Philip Cowie

    2013-01-01

    Full Text Available Modern genetic analysis has shown that most polymorphisms associated with human disease are non-coding. Much of the functional information contained in the non-coding genome consists of cis-regulatory sequences (CRSs that are required to respond to signal transduction cues that direct cell specific gene expression. It has been hypothesised that many diseases may be due to polymorphisms within CRSs that alter their responses to signal transduction cues. However, identification of CRSs, and the effects of allelic variation on their ability to respond to signal transduction cues, is still at an early stage. In the current review we describe the use of comparative genomics and experimental techniques that allow for the identification of CRSs building on recent advances by the ENCODE consortium. In addition we describe techniques that allow for the analysis of the effects of allelic variation and epigenetic modification on CRS responses to signal transduction cues. Using specific examples we show that the interactions driving these elements are highly complex and the effects of disease associated polymorphisms often subtle. It is clear that gaining an understanding of the functions of CRSs, and how they are affected by SNPs and epigenetic modification, is essential to understanding the genetic basis of human disease and stratification whilst providing novel directions for the development of personalised medicine.

  8. cis-regulatory elements involved in ultraviolet light regulation and plant defense.

    Science.gov (United States)

    Wingender, R; Röhrig, H; Höricke, C; Schell, J

    1990-10-01

    An elicitor-regulated transient expression system was established in soybean protoplasts that allowed the identification of cis-regulatory elements involved in plant defense. The 5' region of an ultraviolet (UV) light-inducible and elicitor-inducible chs gene (chs1) of soybean was subjected to deletion analysis with the help of chimeric chs-nptII/gus gene constructs. This analysis delimited the sequences necessary for elicitor inducibility to -175 and -134 of the chs1 promoter. The same soybean sequences were able to direct elicitor inducibility in parsley protoplasts, suggesting a conserved function of cis-acting elements involved in plant defense. In addition, this region of the soybean promoter also promotes UV light inducibility in parsley protoplasts. However, in contrast to the elicitor induction, correct regulation was not observed after UV light induction when sequences downstream of -75 were replaced by a heterologous minimal promoter. This result indicates that at least two cis-acting elements are involved in UV light induction.

  9. Analysis of mammalian cis-regulatory DNA elements by homologous recombination.

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    Fiering, S; Bender, M A; Groudine, M

    1999-01-01

    The use of homologous recombination to modify and thereby functionally analyze cis-regulatory DNA elements in mammalian cells has become an important approach in mammalian gene expression research. We have emphasized the necessity of designing a system that allows the removal of selectable markers used in targeting and facilitates the further modification of the region under study. To perform these tasks, we presently favor making an initial HR-mediated replacement of the entire element under study with an active positive selectable marker in combination with either an inactive second positive selectable marker or an active negative selectable marker. The plug and socket system, in which an inactive selectable marker is complemented by HR, is the most dependable and well-characterized option for making secondary modifications. However, the double-replacement system has certain advantages, and the recently developed RMCE approach, which allows replacement of a negative selectable marker by site-specific recombinase-mediated insertion without using a positive selectable marker, will likely prove very valuable in future experiments. Each of the systems, or combinations thereof, should be considered in light of the specifics of any given experiment to select the most appropriate option. Although the emphasis of this article has been the analysis of cis-acting regulatory elements involved in transcription, these same approaches can be used to analyze other regulatory elements (e.g., origins of replication) and to make multiple subtle mutations in polypeptides.

  10. ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera.

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    Lewis, James J; van der Burg, Karin R L; Mazo-Vargas, Anyi; Reed, Robert D

    2016-09-13

    Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq) annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution.

  11. Single nucleotide polymorphisms with cis-regulatory effects on long non-coding transcripts in human primary monocytes.

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    Jonas Carlsson Almlöf

    Full Text Available We applied genome-wide allele-specific expression analysis of monocytes from 188 samples. Monocytes were purified from white blood cells of healthy blood donors to detect cis-acting genetic variation that regulates the expression of long non-coding RNAs. We analysed 8929 regions harboring genes for potential long non-coding RNA that were retrieved from data from the ENCODE project. Of these regions, 60% were annotated as intergenic, which implies that they do not overlap with protein-coding genes. Focusing on the intergenic regions, and using stringent analysis of the allele-specific expression data, we detected robust cis-regulatory SNPs in 258 out of 489 informative intergenic regions included in the analysis. The cis-regulatory SNPs that were significantly associated with allele-specific expression of long non-coding RNAs were enriched to enhancer regions marked for active or bivalent, poised chromatin by histone modifications. Out of the lncRNA regions regulated by cis-acting regulatory SNPs, 20% (n = 52 were co-regulated with the closest protein coding gene. We compared the identified cis-regulatory SNPs with those in the catalog of SNPs identified by genome-wide association studies of human diseases and traits. This comparison identified 32 SNPs in loci from genome-wide association studies that displayed a strong association signal with allele-specific expression of non-coding RNAs in monocytes, with p-values ranging from 6.7×10(-7 to 9.5×10(-89. The identified cis-regulatory SNPs are associated with diseases of the immune system, like multiple sclerosis and rheumatoid arthritis.

  12. Nucleotide sequence conservation of novel and established cis-regulatory sites within the tyrosine hydroxylase gene promoter.

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    Wang, Meng; Banerjee, Kasturi; Baker, Harriet; Cave, John W

    2015-02-01

    Tyrosine hydroxylase (TH) is the rate-limiting enzyme in catecholamine biosynthesis and its gene proximal promoter ( electromobility shift assays showed that brain-region specific complexes assemble on these motifs. These studies also identified a non-canonical CRE binding (CREB) protein recognition element in the proximal promoter. Together, these studies provide a detailed analysis of evolutionary conservation within the TH promoter and identify potential cis-regulatory motifs that underlie a core set of regulatory mechanisms in mammals.

  13. An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.

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    Liu, Bingqiang; Zhang, Hanyuan; Zhou, Chuan; Li, Guojun; Fennell, Anne; Wang, Guanghui; Kang, Yu; Liu, Qi; Ma, Qin

    2016-08-09

    Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP(3)). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, we collected orthologous genes from available prokaryotic genomes and built the orthologous regulatory regions based on sequence similarity of promoter regions. This procedure made full use of the large-scale genomic data and taxonomy information and filtered out the promoters with limited contribution to produce a high quality orthologous promoter set. The promoter scoring and pruning is implemented through motif voting by a set of complementary predicting tools that mine as many motif candidates as possible and simultaneously eliminate the effect of random noise. We have applied the framework to Escherichia coli k12 genome and evaluated the prediction performance through comparison with seven existing programs. This evaluation was systematically carried out at the nucleotide and binding site level, and the results showed that MP(3) consistently outperformed other popular motif finding tools. We have integrated MP(3) into our motif identification and analysis server DMINDA, allowing users to efficiently identify and analyze motifs in 2,072 completely sequenced prokaryotic genomes. The performance evaluation indicated that MP(3) is effective for predicting regulatory motifs in prokaryotic genomes. Its application may enhance

  14. Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition.

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    Arindam Deb

    Full Text Available Combinations of cis-regulatory elements (CREs present at the promoters facilitate the binding of several transcription factors (TFs, thereby altering the consequent gene expressions. Due to the eminent complexity of the regulatory mechanism, the combinatorics of CRE-mediated transcriptional regulation has been elusive. In this work, we have developed a new methodology that quantifies the co-occurrence tendencies of CREs present in a set of promoter sequences; these co-occurrence scores are filtered in three consecutive steps to test their statistical significance; and the significantly co-occurring CRE pairs are presented as networks. These networks of co-occurring CREs are further transformed to derive higher order of regulatory combinatorics. We have further applied this methodology on the differentially up-regulated gene-sets of rice tissues under fungal (Magnaporthe infected conditions to demonstrate how it helps to understand the CRE-mediated combinatorial gene regulation. Our analysis includes a wide spectrum of biologically important results. The CRE pairs having a strong tendency to co-occur often exhibit very similar joint distribution patterns at the promoters of rice. We couple the network approach with experimental results of plant gene regulation and defense mechanisms and find evidences of auto and cross regulation among TF families, cross-talk among multiple hormone signaling pathways, similarities and dissimilarities in regulatory combinatorics between different tissues, etc. Our analyses have pointed a highly distributed nature of the combinatorial gene regulation facilitating an efficient alteration in response to fungal attack. All together, our proposed methodology could be an important approach in understanding the combinatorial gene regulation. It can be further applied to unravel the tissue and/or condition specific combinatorial gene regulation in other eukaryotic systems with the availability of annotated genomic

  15. Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition.

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    Deb, Arindam; Kundu, Sudip

    2015-01-01

    Combinations of cis-regulatory elements (CREs) present at the promoters facilitate the binding of several transcription factors (TFs), thereby altering the consequent gene expressions. Due to the eminent complexity of the regulatory mechanism, the combinatorics of CRE-mediated transcriptional regulation has been elusive. In this work, we have developed a new methodology that quantifies the co-occurrence tendencies of CREs present in a set of promoter sequences; these co-occurrence scores are filtered in three consecutive steps to test their statistical significance; and the significantly co-occurring CRE pairs are presented as networks. These networks of co-occurring CREs are further transformed to derive higher order of regulatory combinatorics. We have further applied this methodology on the differentially up-regulated gene-sets of rice tissues under fungal (Magnaporthe) infected conditions to demonstrate how it helps to understand the CRE-mediated combinatorial gene regulation. Our analysis includes a wide spectrum of biologically important results. The CRE pairs having a strong tendency to co-occur often exhibit very similar joint distribution patterns at the promoters of rice. We couple the network approach with experimental results of plant gene regulation and defense mechanisms and find evidences of auto and cross regulation among TF families, cross-talk among multiple hormone signaling pathways, similarities and dissimilarities in regulatory combinatorics between different tissues, etc. Our analyses have pointed a highly distributed nature of the combinatorial gene regulation facilitating an efficient alteration in response to fungal attack. All together, our proposed methodology could be an important approach in understanding the combinatorial gene regulation. It can be further applied to unravel the tissue and/or condition specific combinatorial gene regulation in other eukaryotic systems with the availability of annotated genomic sequences and suitable

  16. Studying the functional conservation of cis-regulatory modules and their transcriptional output

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    Bailey Timothy L

    2008-04-01

    Full Text Available Abstract Background Cis-regulatory modules (CRMs are distinct, genomic regions surrounding the target gene that can independently activate the promoter to drive transcription. The activation of a CRM is controlled by the binding of a certain combination of transcription factors (TFs. It would be of great benefit if the transcriptional output mediated by a specific CRM could be predicted. Of equal benefit would be identifying in silico a specific CRM as the driver of the expression in a specific tissue or situation. We extend a recently developed biochemical modeling approach to manage both prediction tasks. Given a set of TFs, their protein concentrations, and the positions and binding strengths of each of the TFs in a putative CRM, the model predicts the transcriptional output of the gene. Our approach predicts the location of the regulating CRM by using predicted TF binding sites in regions near the gene as input to the model and searching for the region that yields a predicted transcription rate most closely matching the known rate. Results Here we show the ability of the model on the example of one of the CRMs regulating the eve gene, MSE2. A model trained on the MSE2 in D. melanogaster was applied to the surrounding sequence of the eve gene in seven other Drosophila species. The model successfully predicts the correct MSE2 location and output in six out of eight Drosophila species we examine. Conclusion The model is able to generalize from D. melanogaster to other Drosophila species and accurately predicts the location and transcriptional output of MSE2 in those species. However, we also show that the current model is not specific enough to function as a genome-wide CRM scanner, because it incorrectly predicts other genomic regions to be MSE2s.

  17. Studying the functional conservation of cis-regulatory modules and their transcriptional output.

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    Bauer, Denis C; Bailey, Timothy L

    2008-04-29

    Cis-regulatory modules (CRMs) are distinct, genomic regions surrounding the target gene that can independently activate the promoter to drive transcription. The activation of a CRM is controlled by the binding of a certain combination of transcription factors (TFs). It would be of great benefit if the transcriptional output mediated by a specific CRM could be predicted. Of equal benefit would be identifying in silico a specific CRM as the driver of the expression in a specific tissue or situation. We extend a recently developed biochemical modeling approach to manage both prediction tasks. Given a set of TFs, their protein concentrations, and the positions and binding strengths of each of the TFs in a putative CRM, the model predicts the transcriptional output of the gene. Our approach predicts the location of the regulating CRM by using predicted TF binding sites in regions near the gene as input to the model and searching for the region that yields a predicted transcription rate most closely matching the known rate. Here we show the ability of the model on the example of one of the CRMs regulating the eve gene, MSE2. A model trained on the MSE2 in D. melanogaster was applied to the surrounding sequence of the eve gene in seven other Drosophila species. The model successfully predicts the correct MSE2 location and output in six out of eight Drosophila species we examine. The model is able to generalize from D. melanogaster to other Drosophila species and accurately predicts the location and transcriptional output of MSE2 in those species. However, we also show that the current model is not specific enough to function as a genome-wide CRM scanner, because it incorrectly predicts other genomic regions to be MSE2s.

  18. Conserved Cis-Regulatory Modules Control Robustness in Msx1 Expression at Single-Cell Resolution

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    Vance, Keith W.; Woodcock, Dan J.; Reid, John E.; Bretschneider, Till; Ott, Sascha; Koentges, Georgy

    2015-01-01

    The process of transcription is highly stochastic leading to cell-to-cell variations and noise in gene expression levels. However, key essential genes have to be precisely expressed at the correct amount and time to ensure proper cellular development and function. Studies in yeast and bacterial systems have shown that gene expression noise decreases as mean expression levels increase, a relationship that is controlled by promoter DNA sequence. However, the function of distal cis-regulatory modules (CRMs), an evolutionary novelty of metazoans, in controlling transcriptional robustness and variability is poorly understood. In this study, we used live cell imaging of transfected reporters combined with a mathematical modelling and statistical inference scheme to quantify the function of conserved Msx1 CRMs and promoters in modulating single-cell real-time transcription rates in C2C12 mouse myoblasts. The results show that the mean expression–noise relationship is solely promoter controlled for this key pluripotency regulator. In addition, we demonstrate that CRMs modulate single-cell basal promoter rate distributions in a graded manner across a population of cells. This extends the rheostatic model of CRM action to provide a more detailed understanding of CRM function at single-cell resolution. We also identify a novel CRM transcriptional filter function that acts to reduce intracellular variability in transcription rates and show that this can be phylogenetically separable from rate modulating CRM activities. These results are important for understanding how the expression of key vertebrate developmental transcription factors is precisely controlled both within and between individual cells. PMID:26342140

  19. Recurrent modification of a conserved cis-regulatory element underlies fruit fly pigmentation diversity.

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    William A Rogers

    2013-08-01

    Full Text Available The development of morphological traits occurs through the collective action of networks of genes connected at the level of gene expression. As any node in a network may be a target of evolutionary change, the recurrent targeting of the same node would indicate that the path of evolution is biased for the relevant trait and network. Although examples of parallel evolution have implicated recurrent modification of the same gene and cis-regulatory element (CRE, little is known about the mutational and molecular paths of parallel CRE evolution. In Drosophila melanogaster fruit flies, the Bric-à-brac (Bab transcription factors control the development of a suite of sexually dimorphic traits on the posterior abdomen. Female-specific Bab expression is regulated by the dimorphic element, a CRE that possesses direct inputs from body plan (ABD-B and sex-determination (DSX transcription factors. Here, we find that the recurrent evolutionary modification of this CRE underlies both intraspecific and interspecific variation in female pigmentation in the melanogaster species group. By reconstructing the sequence and regulatory activity of the ancestral Drosophila melanogaster dimorphic element, we demonstrate that a handful of mutations were sufficient to create independent CRE alleles with differing activities. Moreover, intraspecific and interspecific dimorphic element evolution proceeded with little to no alterations to the known body plan and sex-determination regulatory linkages. Collectively, our findings represent an example where the paths of evolution appear biased to a specific CRE, and drastic changes in function were accompanied by deep conservation of key regulatory linkages.

  20. Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models.

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    Dmitry Svetlichnyy

    2015-11-01

    Full Text Available Cancer genomes contain vast amounts of somatic mutations, many of which are passenger mutations not involved in oncogenesis. Whereas driver mutations in protein-coding genes can be distinguished from passenger mutations based on their recurrence, non-coding mutations are usually not recurrent at the same position. Therefore, it is still unclear how to identify cis-regulatory driver mutations, particularly when chromatin data from the same patient is not available, thus relying only on sequence and expression information. Here we use machine-learning methods to predict functional regulatory regions using sequence information alone, and compare the predicted activity of the mutated region with the reference sequence. This way we define the Predicted Regulatory Impact of a Mutation in an Enhancer (PRIME. We find that the recently identified driver mutation in the TAL1 enhancer has a high PRIME score, representing a "gain-of-target" for MYB, whereas the highly recurrent TERT promoter mutation has a surprisingly low PRIME score. We trained Random Forest models for 45 cancer-related transcription factors, and used these to score variations in the HeLa genome and somatic mutations across more than five hundred cancer genomes. Each model predicts only a small fraction of non-coding mutations with a potential impact on the function of the encompassing regulatory region. Nevertheless, as these few candidate driver mutations are often linked to gains in chromatin activity and gene expression, they may contribute to the oncogenic program by altering the expression levels of specific oncogenes and tumor suppressor genes.

  1. Putative cis-regulatory elements associated with heat shock genes activated during excystation of Cryptosporidium parvum.

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    Benjamin Cohn

    Full Text Available BACKGROUND: Cryptosporidiosis is a ubiquitous infectious disease, caused by the protozoan parasites Cryptosporidium hominis and C. parvum, leading to acute, persistent and chronic diarrhea worldwide. Although the complications of this disease can be serious, even fatal, in immunocompromised patients of any age, they have also been found to lead to long term effects, including growth inhibition and impaired cognitive development, in infected immunocompetent children. The Cryptosporidium life cycle alternates between a dormant stage, the oocyst, and a highly replicative phase that includes both asexual vegetative stages as well as sexual stages, implying fine genetic regulatory mechanisms. The parasite is extremely difficult to study because it cannot be cultured in vitro and animal models are equally challenging. The recent publication of the genome sequence of C. hominis and C. parvum has, however, significantly advanced our understanding of the biology and pathogenesis of this parasite. METHODOLOGY/PRINCIPAL FINDINGS: Herein, our goal was to identify cis-regulatory elements associated with heat shock response in Cryptosporidium using a combination of in silico and real time RT-PCR strategies. Analysis with Gibbs-Sampling algorithms of upstream non-translated regions of twelve genes annotated as heat shock proteins in the Cryptosporidium genome identified a highly conserved over-represented sequence motif in eleven of them. RT-PCR analyses, described herein and also by others, show that these eleven genes bearing the putative element are induced concurrent with excystation of parasite oocysts via heat shock. CONCLUSIONS/SIGNIFICANCE: Our analyses suggest that occurrences of a motif identified in the upstream regions of the Cryptosporidium heat shock genes represent parts of the transcriptional apparatus and function as stress response elements that activate expression of these genes during excystation, and possibly at other stages in the life

  2. cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer Independent

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    Yue Huang

    2017-03-01

    Full Text Available Alterations in distal regulatory elements that control gene expression underlie many diseases, including cancer. Epigenomic analyses of normal and diseased cells have produced correlative predictions for connections between dysregulated enhancers and target genes involved in pathogenesis. However, with few exceptions, these predicted cis-regulatory circuits remain untested. Here, we dissect cis-regulatory circuits that lead to overexpression of NEK6, a mitosis-associated kinase, in human B cell lymphoma. We find that only a minor subset of predicted enhancers is required for NEK6 expression. Indeed, an annotated super-enhancer is dispensable for NEK6 overexpression and for maintaining the architecture of a B cell-specific regulatory hub. A CTCF cluster serves as a chromatin and architectural boundary to block communication of the NEK6 regulatory hub with neighboring genes. Our findings emphasize that validation of predicted cis-regulatory circuits and super-enhancers is needed to prioritize transcriptional control elements as therapeutic targets.

  3. cis-Regulatory control of three cell fate-specific genes in vulval organogenesis of Caenorhabditis elegans and C. briggsae.

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    Kirouac, Martha; Sternberg, Paul W

    2003-05-01

    The great-grandprogeny of the Caenorhabditis elegans vulval precursor cells (VPCs) adopt one of the final vulA, B1, B2, C, D, E, and F cell fates in a precise spatial pattern. This pattern of vulval cell types is likely to depend on the cis-regulatory regions of the transcriptional targets of intercellular signals in vulval development. egl-17, zmp-1, and cdh-3 are expressed differentially in the developing vulva cells, providing a potential readout for different signaling pathways. To understand how such pathways interact to specify unique vulval cell types in a precise pattern, we have identified cis-regulatory regions sufficient to confer vulval cell type-specific regulation when fused in cis to the basal pes-10 promoter. We have identified the C. briggsae homologs of these three genes, with their corresponding control regions, and tested these regions in both C. elegans and C. briggsae. These regions of similarity in C. elegans and C. briggsae upstream of egl-17, zmp-1, and cdh-3 promote expression in vulval cells and the anchor cell (AC). By using the cis-regulatory analysis and phylogenetic footprinting, we have identified overrepresented sequences involved in conferring vulval and AC expression.

  4. cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer Independent.

    Science.gov (United States)

    Huang, Yue; Koues, Olivia I; Zhao, Jiang-Yang; Liu, Regina; Pyfrom, Sarah C; Payton, Jacqueline E; Oltz, Eugene M

    2017-03-21

    Alterations in distal regulatory elements that control gene expression underlie many diseases, including cancer. Epigenomic analyses of normal and diseased cells have produced correlative predictions for connections between dysregulated enhancers and target genes involved in pathogenesis. However, with few exceptions, these predicted cis-regulatory circuits remain untested. Here, we dissect cis-regulatory circuits that lead to overexpression of NEK6, a mitosis-associated kinase, in human B cell lymphoma. We find that only a minor subset of predicted enhancers is required for NEK6 expression. Indeed, an annotated super-enhancer is dispensable for NEK6 overexpression and for maintaining the architecture of a B cell-specific regulatory hub. A CTCF cluster serves as a chromatin and architectural boundary to block communication of the NEK6 regulatory hub with neighboring genes. Our findings emphasize that validation of predicted cis-regulatory circuits and super-enhancers is needed to prioritize transcriptional control elements as therapeutic targets.

  5. Changes in cis-regulatory elements of a key floral regulator are associated with divergence of inflorescence architectures.

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    Kusters, Elske; Della Pina, Serena; Castel, Rob; Souer, Erik; Koes, Ronald

    2015-08-15

    Higher plant species diverged extensively with regard to the moment (flowering time) and position (inflorescence architecture) at which flowers are formed. This seems largely caused by variation in the expression patterns of conserved genes that specify floral meristem identity (FMI), rather than changes in the encoded proteins. Here, we report a functional comparison of the promoters of homologous FMI genes from Arabidopsis, petunia, tomato and Antirrhinum. Analysis of promoter-reporter constructs in petunia and Arabidopsis, as well as complementation experiments, showed that the divergent expression of leafy (LFY) and the petunia homolog aberrant leaf and flower (ALF) results from alterations in the upstream regulatory network rather than cis-regulatory changes. The divergent expression of unusual floral organs (UFO) from Arabidopsis, and the petunia homolog double top (DOT), however, is caused by the loss or gain of cis-regulatory promoter elements, which respond to trans-acting factors that are expressed in similar patterns in both species. Introduction of pUFO:UFO causes no obvious defects in Arabidopsis, but in petunia it causes the precocious and ectopic formation of flowers. This provides an example of how a change in a cis-regulatory region can account for a change in the plant body plan.

  6. Characterization of "cis"-regulatory elements ("c"RE) associated with mammary gland function

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    The Bos taurus genome assembly has propelled dairy science into a new era; still, most of the information encoded in the genome has not yet been decoded. The human Encyclopedia of DNA Elements (ENCODE) project has spearheaded the identification and annotation of functional genomic elements in the hu...

  7. Prioritizing predicted cis-regulatory elements for co-expressed gene sets based on Lasso regression models.

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    Hu, Hong; Roqueiro, Damian; Dai, Yang

    2011-01-01

    Computational prediction of cis-regulatory elements for a set of co-expressed genes based on sequence analysis provides an overwhelming volume of potential transcription factor binding sites. It presents a challenge to prioritize transcription factors for regulatory functional studies. A novel approach based on the use of Lasso regression models is proposed to address this problem. We examine the ability of the Lasso model using time-course microarray data obtained from a comprehensive study of gene expression profiles in skin and mucosal wounds in mouse over all stages of wound healing.

  8. A transposon-based chromosomal engineering method to survey a large cis-regulatory landscape in mice.

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    Kokubu, Chikara; Horie, Kyoji; Abe, Koichiro; Ikeda, Ryuji; Mizuno, Sumi; Uno, Yoshihiro; Ogiwara, Sanae; Ohtsuka, Masato; Isotani, Ayako; Okabe, Masaru; Imai, Kenji; Takeda, Junji

    2009-08-01

    A large cis-regulatory landscape is a common feature of vertebrate genomes, particularly at key developmental gene loci with finely tuned expression patterns. Existing genetic tools for surveying large genomic regions of interest spanning over hundreds of kilobases are limited. Here we propose a chromosomal engineering strategy exploiting the local hopping trait of the Sleeping Beauty transposon in the mouse genome. We generated embryonic stem cells with a targeted integration of the transposon vector, carrying an enhancer-detecting lacZ reporter and loxP cassette, into the developmentally critical Pax1 gene locus, followed by efficient local transpositions, nested deletion formation and derivation of embryos by tetraploid complementation. Comparative reporter expression analysis among different insertion/deletion embryos substantially facilitated long-range cis-regulatory element mapping in the genomic neighborhood and demonstrated the potential of the transposon-based approach as a versatile tool for exploration of defined genomic intervals of functional or clinical relevance, such as disease-associated microdeletions.

  9. Characterization of a putative cis-regulatory element that controls transcriptional activity of the pig uroplakin II gene promoter.

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    Kwon, Deug-Nam; Park, Mi-Ryung; Park, Jong-Yi; Cho, Ssang-Goo; Park, Chankyu; Oh, Jae-Wook; Song, Hyuk; Kim, Jae-Hwan; Kim, Jin-Hoi

    2011-07-01

    Uroplakin II (UPII) is a one of the integral membrane proteins synthesized as a major differentiation product of mammalian urothelium. UPII gene expression is bladder specific and differentiation dependent, but little is known about its transcription response elements and molecular mechanism. To identify the cis-regulatory elements in the pig UPII (pUPII) gene promoter region, we constructed pUPII 5' upstream region deletion mutants and demonstrated that each of the deletion mutants participates in controlling the expression of the pUPII gene in human bladder carcinoma RT4 cells. We also identified a new core promoter region and putative negative cis-regulatory element within a minimal promoter region. In addition, we showed that hepatocyte nuclear factor 4 (HNF4) can directly bind in the pUPII core promoter (5F-1) region, which plays a critical role in controlling promoter activity. Transient cotransfection experiments showed that HNF4 positively regulates pUPII gene promoter activity. Thus, the binding element and its binding protein, HNF4 transcription factor, may be involved in the mechanism that specifically regulates pUPII gene transcription.

  10. ChIP-Seq-Annotated Heliconius erato Genome Highlights Patterns of cis-Regulatory Evolution in Lepidoptera

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    James J. Lewis

    2016-09-01

    Full Text Available Uncovering phylogenetic patterns of cis-regulatory evolution remains a fundamental goal for evolutionary and developmental biology. Here, we characterize the evolution of regulatory loci in butterflies and moths using chromatin immunoprecipitation sequencing (ChIP-seq annotation of regulatory elements across three stages of head development. In the process we provide a high-quality, functionally annotated genome assembly for the butterfly, Heliconius erato. Comparing cis-regulatory element conservation across six lepidopteran genomes, we find that regulatory sequences evolve at a pace similar to that of protein-coding regions. We also observe that elements active at multiple developmental stages are markedly more conserved than elements with stage-specific activity. Surprisingly, we also find that stage-specific proximal and distal regulatory elements evolve at nearly identical rates. Our study provides a benchmark for genome-wide patterns of regulatory element evolution in insects, and it shows that developmental timing of activity strongly predicts patterns of regulatory sequence evolution.

  11. Creation of cis-regulatory elements during sea urchin evolution by co-option and optimization of a repetitive sequence adjacent to the spec2a gene.

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    Dayal, Sandeep; Kiyama, Takae; Villinski, Jeffrey T; Zhang, Ning; Liang, Shuguang; Klein, William H

    2004-09-15

    The creation, preservation, and degeneration of cis-regulatory elements controlling developmental gene expression are fundamental genome-level evolutionary processes about which little is known. Here, we identify critical differences in cis-regulatory elements controlling the expression of the sea urchin aboral ectoderm-specific spec genes. We found multiple copies of a repetitive sequence element termed RSR in genomes of species within the Strongylocentrotidae family, but RSRs were not detected in genomes of species outside Strongylocentrotidae. spec genes in Strongylocentrotus purpuratus are invariably associated with RSRs, and the spec2a RSR functioned as a transcriptional enhancer and displayed greater activity than did spec1 or spec2c RSRs. Single-base pair differences at two cis-regulatory elements within the spec2a RSR increased the binding affinities of four transcription factors, SpCCAAT-binding factor at one element and SpOtx, SpGoosecoid, and SpGATA-E at another. The cis-regulatory elements to which these four factors bound were recent evolutionary acquisitions that acted to either activate or repress transcription, depending on the cell type. These elements were found in the spec2a RSR ortholog in Strongylocentrotus pallidus but not in RSR orthologs of Strongylocentrotus droebachiensis or Hemicentrotus pulcherrimus. Our results indicated that a dynamic pattern of cis-regulatory element evolution exists for spec genes despite their conserved aboral ectoderm expression.

  12. Shared Enhancer Activity in the Limbs and Phallus and Functional Divergence of a Limb-Genital cis-Regulatory Element in Snakes.

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    Infante, Carlos R; Mihala, Alexandra G; Park, Sungdae; Wang, Jialiang S; Johnson, Kenji K; Lauderdale, James D; Menke, Douglas B

    2015-10-12

    The amniote phallus and limbs differ dramatically in their morphologies but share patterns of signaling and gene expression in early development. Thus far, the extent to which genital and limb transcriptional networks also share cis-regulatory elements has remained unexplored. We show that many limb enhancers are retained in snake genomes, suggesting that these elements may function in non-limb tissues. Consistent with this, our analysis of cis-regulatory activity in mice and Anolis lizards reveals that patterns of enhancer activity in embryonic limbs and genitalia overlap heavily. In mice, deletion of HLEB, an enhancer of Tbx4, produces defects in hindlimbs and genitalia, establishing the importance of this limb-genital enhancer for development of these different appendages. Further analyses demonstrate that the HLEB of snakes has lost hindlimb enhancer function while retaining genital activity. Our findings identify roles for Tbx4 in genital development and highlight deep similarities in cis-regulatory activity between limbs and genitalia.

  13. Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules.

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    Sergei A Filichkin

    Full Text Available BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day. Synchronized transcriptome cycling is driven through an extensive network of diurnal and clock-regulated transcription factors and their target cis-regulatory elements. Study of the cycling transcriptome in other plant species could thus help elucidate the similarities and differences and identify hubs of regulation common to monocot and dicot plants. METHODOLOGY/PRINCIPAL FINDINGS: Using a combination of oligonucleotide microarrays and data mining pipelines, we examined daily rhythms in gene expression in one monocotyledonous and one dicotyledonous plant, rice and poplar, respectively. Cycling transcriptomes were interrogated under different diurnal (driven and circadian (free running light and temperature conditions. Collectively, photocycles and thermocycles regulated about 60% of the expressed nuclear genes in rice and poplar. Depending on the condition tested, up to one third of oscillating Arabidopsis-poplar-rice orthologs were phased within three hours of each other suggesting a high degree of conservation in terms of rhythmic gene expression. We identified clusters of rhythmically co-expressed genes and searched their promoter sequences to identify phase-specific cis-elements, including elements that were conserved in the promoters of Arabidopsis, poplar, and rice. CONCLUSIONS/SIGNIFICANCE: Our results show that the cycling patterns of many circadian clock genes are highly conserved across poplar, rice, and Arabidopsis. The expression of many orthologous genes in key metabolic and regulatory pathways is diurnal and/or circadian regulated and phased to similar times of day. Our results confirm

  14. Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular-weight glutenin subunits.

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    Ravel, Catherine; Fiquet, Samuel; Boudet, Julie; Dardevet, Mireille; Vincent, Jonathan; Merlino, Marielle; Michard, Robin; Martre, Pierre

    2014-01-01

    The concentration and composition of the gliadin and glutenin seed storage proteins (SSPs) in wheat flour are the most important determinants of its end-use value. In cereals, the synthesis of SSPs is predominantly regulated at the transcriptional level by a complex network involving at least five cis-elements in gene promoters. The high-molecular-weight glutenin subunits (HMW-GS) are encoded by two tightly linked genes located on the long arms of group 1 chromosomes. Here, we sequenced and annotated the HMW-GS gene promoters of 22 electrophoretic wheat alleles to identify putative cis-regulatory motifs. We focused on 24 motifs known to be involved in SSP gene regulation. Most of them were identified in at least one HMW-GS gene promoter sequence. A common regulatory framework was observed in all the HMW-GS gene promoters, as they shared conserved cis-regulatory modules (CCRMs) including all the five motifs known to regulate the transcription of SSP genes. This common regulatory framework comprises a composite box made of the GATA motifs and GCN4-like Motifs (GLMs) and was shown to be functional as the GLMs are able to bind a bZIP transcriptional factor SPA (Storage Protein Activator). In addition to this regulatory framework, each HMW-GS gene promoter had additional motifs organized differently. The promoters of most highly expressed x-type HMW-GS genes contain an additional box predicted to bind R2R3-MYB transcriptional factors. However, the differences in annotation between promoter alleles could not be related to their level of expression. In summary, we identified a common modular organization of HMW-GS gene promoters but the lack of correlation between the cis-motifs of each HMW-GS gene promoter and their level of expression suggests that other cis-elements or other mechanisms regulate HMW-GS gene expression.

  15. MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs

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    Tsunoda Tatsuhiko

    2007-03-01

    Full Text Available Abstract Background A combination of multiple types of transcription factors and cis-regulatory elements is often required for gene expression in eukaryotes, and the combinatorial regulation confers specific gene expression to tissues or environments. To reveal the combinatorial regulation, computational methods are developed that efficiently infer combinations of cis-regulatory motifs that are important for gene expression as measured by DNA microarrays. One promising type of computational method is to utilize regression analysis between expression levels and scores of motifs in input sequences. This type takes full advantage of information on expression levels because it does not require that the expression level of each gene be dichotomized according to whether or not it reaches a certain threshold level. However, there is no web-based tool that employs regression methods to systematically search for motif combinations and that practically handles combinations of more than two or three motifs. Results We here introduced MotifCombinator, an online tool with a user-friendly interface, to systematically search for combinations composed of any number of motifs based on regression methods. The tool utilizes well-known regression methods (the multivariate linear regression, the multivariate adaptive regression spline or MARS, and the multivariate logistic regression method for this purpose, and uses the genetic algorithm to search for combinations composed of any desired number of motifs. The visualization systems in this tool help users to intuitively grasp the process of the combination search, and the backup system allows users to easily stop and restart calculations that are expected to require large computational time. This tool also provides preparatory steps needed for systematic combination search – i.e., selecting single motifs to constitute combinations and cutting out redundant similar motifs based on clustering analysis. Conclusion

  16. Separate elements of the TERMINAL FLOWER 1 cis-regulatory region integrate pathways to control flowering time and shoot meristem identity.

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    Serrano-Mislata, Antonio; Fernández-Nohales, Pedro; Doménech, María J; Hanzawa, Yoshie; Bradley, Desmond; Madueño, Francisco

    2016-09-15

    TERMINAL FLOWER 1 (TFL1) is a key regulator of Arabidopsis plant architecture that responds to developmental and environmental signals to control flowering time and the fate of shoot meristems. TFL1 expression is dynamic, being found in all shoot meristems, but not in floral meristems, with the level and distribution changing throughout development. Using a variety of experimental approaches we have analysed the TFL1 promoter to elucidate its functional structure. TFL1 expression is based on distinct cis-regulatory regions, the most important being located 3' of the coding sequence. Our results indicate that TFL1 expression in the shoot apical versus lateral inflorescence meristems is controlled through distinct cis-regulatory elements, suggesting that different signals control expression in these meristem types. Moreover, we identified a cis-regulatory region necessary for TFL1 expression in the vegetative shoot and required for a wild-type flowering time, supporting that TFL1 expression in the vegetative meristem controls flowering time. Our study provides a model for the functional organisation of TFL1 cis-regulatory regions, contributing to our understanding of how developmental pathways are integrated at the genomic level of a key regulator to control plant architecture. © 2016. Published by The Company of Biologists Ltd.

  17. Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position

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    Lang Michael

    2010-11-01

    Full Text Available Abstract Background The modern coelacanth (Latimeria is the extant taxon of a basal sarcopterygian lineage and sister group to tetrapods. Apart from certain apomorphic traits, its morphology is characterized by a high degree of retention of ancestral vertebrate structures and little morphological change. An insight into the molecular evolution that may explain the unchanged character of Latimeria morphology requires the analysis of the expression patterns of developmental regulator genes and their cis-regulatory modules (CRMs. Results We describe the comparative and functional analysis of the sonic hedgehog (shh genomic region of Latimeria menadoensis. Several putative enhancers in the Latimeria shh locus have been identified by comparisons to sarcopterygian and actinopterygian extant species. Specific sequence conservation with all known actinopterygian enhancer elements has been detected. However, these elements are selectively missing in more recently diverged actinopterygian and sarcopterygian species. The functionality of the putative Latimeria enhancers was confirmed by reporter gene expression analysis in transient transgenic zebrafish and chick embryos. Conclusions Latimeria shh CRMs represent the ancestral set of enhancers that have emerged before the split of lobe-finned and ray-finned fishes. In contrast to lineage-specific losses and differentiations in more derived lineages, Latimeria shh enhancers reveal low levels of sequence diversification. High overall sequence conservation of shh conserved noncoding elements (CNE is consistent with the general trend of high levels of conservation of noncoding DNA in the slowly evolving Latimeria genome.

  18. Ancient polymorphism and functional variation in the primate MHC-DQA1 5' cis-regulatory region.

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    Loisel, Dagan A; Rockman, Matthew V; Wray, Gregory A; Altmann, Jeanne; Alberts, Susan C

    2006-10-31

    Precise regulation of MHC gene expression is critical to vertebrate immune surveillance and response. Polymorphisms in the 5' proximal promoter region of the human class II gene HLA-DQA1 have been shown to influence its transcriptional regulation and may contribute to the pathogenesis of autoimmune diseases. We investigated the evolutionary history of this cis-regulatory region by sequencing the DQA1 5' proximal promoter region in eight nonhuman primate species. We observed unexpectedly high levels of sequence variation and multiple strong signatures of balancing selection in this region. Specifically, the considerable DQA1 promoter region diversity was characterized by abundant shared (or trans-species) polymorphism and a pronounced lack of fixed differences between species. The majority of transcription factor binding sites in the DQA1 promoter region were polymorphic within species, and these binding site polymorphisms were commonly shared among multiple species despite evidence for negative selection eliminating a significant fraction of binding site mutations. We assessed the functional consequences of intraspecific promoter region diversity using a cell line-based reporter assay and detected significant differences among baboon DQA1 promoter haplotypes in their ability to drive transcription in vitro. The functional differentiation of baboon promoter haplotypes, together with the significant deviations from neutral sequence evolution, suggests a role for balancing selection in the evolution of DQA1 transcriptional regulation in primates.

  19. A comparative analysis of the evolution, expression, and cis-regulatory element of polygalacturonase genes in grasses and dicots.

    Science.gov (United States)

    Liang, Ying; Yu, Youjian; Cui, Jinlong; Lyu, Meiling; Xu, Liai; Cao, Jiashu

    2016-11-01

    Cell walls are a distinguishing characteristic of plants essential to their survival. The pectin content of primary cell walls in grasses and dicots is distinctly different. Polygalacturonases (PGs) can degrade pectins and participate in multiple developmental processes of plants. This study comprehensively compared the evolution, expression, and cis-regulatory element of PGs in grasses and dicots. A total of 577 PGs identified from five grasses and five dicots fell into seven clades. Evolutionary analysis demonstrated the distinct differences between grasses and dicots in patterns of gene duplication and loss, and evolutionary rates. Grasses generally contained much fewer clade C and F members than dicots. We found that this disparity was the result of less duplication and more gene losses in grasses. More duplications occurred in clades D and E, and expression analysis showed that most of clade E members were expressed ubiquitously at a high overall level and clade D members were closely related to male reproduction in both grasses and dicots, suggesting their biological functions were highly conserved across species. In addition to the general role in reproductive development, PGs of clades C and F specifically played roles in root development in dicots, shedding light on organ differentiation between the two groups of plants. A regulatory element analysis of clade C and F members implied that possible functions of PGs in specific biological responses contributed to their expansion and preservation. This work can improve the knowledge of PGs in plants generally and in grasses specifically and is beneficial to functional studies.

  20. Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period

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    Tena, Juan J.; González-Aguilera, Cristina; Fernández-Miñán, Ana; Vázquez-Marín, Javier; Parra-Acero, Helena; Cross, Joe W.; Rigby, Peter W.J.; Carvajal, Jaime J.; Wittbrodt, Joachim; Gómez-Skarmeta, José L.; Martínez-Morales, Juan R.

    2014-01-01

    The complex relationship between ontogeny and phylogeny has been the subject of attention and controversy since von Baer’s formulations in the 19th century. The classic concept that embryogenesis progresses from clade general features to species-specific characters has often been revisited. It has become accepted that embryos from a clade show maximum morphological similarity at the so-called phylotypic period (i.e., during mid-embryogenesis). According to the hourglass model, body plan conservation would depend on constrained molecular mechanisms operating at this period. More recently, comparative transcriptomic analyses have provided conclusive evidence that such molecular constraints exist. Examining cis-regulatory architecture during the phylotypic period is essential to understand the evolutionary source of body plan stability. Here we compare transcriptomes and key epigenetic marks (H3K4me3 and H3K27ac) from medaka (Oryzias latipes) and zebrafish (Danio rerio), two distantly related teleosts separated by an evolutionary distance of 115–200 Myr. We show that comparison of transcriptome profiles correlates with anatomical similarities and heterochronies observed at the phylotypic stage. Through comparative epigenomics, we uncover a pool of conserved regulatory regions (≈700), which are active during the vertebrate phylotypic period in both species. Moreover, we show that their neighboring genes encode mainly transcription factors with fundamental roles in tissue specification. We postulate that these regulatory regions, active in both teleost genomes, represent key constrained nodes of the gene networks that sustain the vertebrate body plan. PMID:24709821

  1. Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules.

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    Bin Z He

    2011-04-01

    Full Text Available Transcription factor binding site(s (TFBS gain and loss (i.e., turnover is a well-documented feature of cis-regulatory module (CRM evolution, yet little attention has been paid to the evolutionary force(s driving this turnover process. The predominant view, motivated by its widespread occurrence, emphasizes the importance of compensatory mutation and genetic drift. Positive selection, in contrast, although it has been invoked in specific instances of adaptive gene expression evolution, has not been considered as a general alternative to neutral compensatory evolution. In this study we evaluate the two hypotheses by analyzing patterns of single nucleotide polymorphism in the TFBS of well-characterized CRM in two closely related Drosophila species, Drosophila melanogaster and Drosophila simulans. An important feature of the analysis is classification of TFBS mutations according to the direction of their predicted effect on binding affinity, which allows gains and losses to be evaluated independently along the two phylogenetic lineages. The observed patterns of polymorphism and divergence are not compatible with neutral evolution for either class of mutations. Instead, multiple lines of evidence are consistent with contributions of positive selection to TFBS gain and loss as well as purifying selection in its maintenance. In discussion, we propose a model to reconcile the finding of selection driving TFBS turnover with constrained CRM function over long evolutionary time.

  2. Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis.

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    Cao, Chensi; Xu, Jiajia; Zheng, Guangyong; Zhu, Xin-Guang

    2016-03-08

    C4 photosynthesis evolved from C3 photosynthesis and has higher light, water, and nitrogen use efficiencies. Several C4 photosynthesis genes show cell-specific expression patterns, which are required for these high resource-use efficiencies. However, the mechanisms underlying the evolution of cis-regulatory elements that control these cell-specific expression patterns remain elusive. In the present study, we tested the hypothesis that the cis-regulatory motifs related to C4 photosynthesis genes were recruited from non-photosynthetic genes and further examined potential mechanisms facilitating this recruitment. We examined 65 predicted bundle sheath cell-specific motifs, 17 experimentally validated cell-specific cis-regulatory elements, and 1,034 motifs derived from gene regulatory networks. Approximately 7, 5, and 1,000 of these three categories of motifs, respectively, were apparently recruited during the evolution of C4 photosynthesis. In addition, we checked 1) the distance between the acceptors and the donors of potentially recruited motifs in a chromosome, and 2) whether the potentially recruited motifs reside within the overlapping region of transposable elements and the promoter of donor genes. The results showed that 7, 4, and 658 of the potentially recruited motifs might have moved via the transposable elements. Furthermore, the potentially recruited motifs showed higher binding affinity to transcription factors compared to randomly generated sequences of the same length as the motifs. This study provides molecular evidence supporting the hypothesis that transposon-driven recruitment of pre-existing cis-regulatory elements from non-photosynthetic genes into photosynthetic genes plays an important role during C4 evolution. The findings of the present study coincide with the observed repetitive emergence of C4 during evolution.

  3. Expression, subcellular localization, and cis-regulatory structure of duplicated phytoene synthase genes in melon (Cucumis melo L.).

    Science.gov (United States)

    Qin, Xiaoqiong; Coku, Ardian; Inoue, Kentaro; Tian, Li

    2011-10-01

    Carotenoids perform many critical functions in plants, animals, and humans. It is therefore important to understand carotenoid biosynthesis and its regulation in plants. Phytoene synthase (PSY) catalyzes the first committed and rate-limiting step in carotenoid biosynthesis. While PSY is present as a single copy gene in Arabidopsis, duplicated PSY genes have been identified in many economically important monocot and dicot crops. CmPSY1 was previously identified from melon (Cucumis melo L.), but was not functionally characterized. We isolated a second PSY gene, CmPSY2, from melon in this work. CmPSY2 possesses a unique intron/exon structure that has not been observed in other plant PSYs. Both CmPSY1 and CmPSY2 are functional in vitro, but exhibit distinct expression patterns in different melon tissues and during fruit development, suggesting differential regulation of the duplicated melon PSY genes. In vitro chloroplast import assays verified the plastidic localization of CmPSY1 and CmPSY2 despite the lack of an obvious plastid target peptide in CmPSY2. Promoter motif analysis of the duplicated melon and tomato PSY genes and the Arabidopsis PSY revealed distinctive cis-regulatory structures of melon PSYs and identified gibberellin-responsive motifs in all PSYs except for SlPSY1, which has not been reported previously. Overall, these data provide new insights into the evolutionary history of plant PSY genes and the regulation of PSY expression by developmental and environmental signals that may involve different regulatory networks.

  4. An arthropod cis-regulatory element functioning in sensory organ precursor development dates back to the Cambrian

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    Simpson Pat

    2010-09-01

    Full Text Available Abstract Background An increasing number of publications demonstrate conservation of function of cis-regulatory elements without sequence similarity. In invertebrates such functional conservation has only been shown for closely related species. Here we demonstrate the existence of an ancient arthropod regulatory element that functions during the selection of neural precursors. The activity of genes of the achaete-scute (ac-sc family endows cells with neural potential. An essential, conserved characteristic of proneural genes is their ability to restrict their own activity to single or a small number of progenitor cells from their initially broad domains of expression. This is achieved through a process called lateral inhibition. A regulatory element, the sensory organ precursor enhancer (SOPE, is required for this process. First identified in Drosophila, the SOPE contains discrete binding sites for four regulatory factors. The SOPE of the Drosophila asense gene is situated in the 5' UTR. Results Through a manual comparison of consensus binding site sequences we have been able to identify a SOPE in UTR sequences of asense-like genes in species belonging to all four arthropod groups (Crustacea, Myriapoda, Chelicerata and Insecta. The SOPEs of the spider Cupiennius salei and the insect Tribolium castaneum are shown to be functional in transgenic Drosophila. This would place the origin of this regulatory sequence as far back as the last common ancestor of the Arthropoda, that is, in the Cambrian, 550 million years ago. Conclusions The SOPE is not detectable by inter-specific sequence comparison, raising the possibility that other ancient regulatory modules in invertebrates might have escaped detection.

  5. Nutritional control of gene expression in Drosophila larvae via TOR, Myc and a novel cis-regulatory element

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    Grewal Savraj S

    2010-01-01

    Full Text Available Abstract Background Nutrient availability is a key determinant of eukaryotic cell growth. In unicellular organisms many signaling and transcriptional networks link nutrient availability to the expression of metabolic genes required for growth. However, less is known about the corresponding mechanisms that operate in metazoans. We used gene expression profiling to explore this issue in developing Drosophila larvae. Results We found that starvation for dietary amino acids (AA's leads to dynamic changes in transcript levels of many metabolic genes. The conserved insulin/PI3K and TOR signaling pathways mediate nutrition-dependent growth in Drosophila and other animals. We found that many AA starvation-responsive transcripts were also altered in TOR mutants. In contrast, although PI3K overexpression induced robust changes in the expression of many metabolic genes, these changes showed limited overlap with the AA starvation expression profile. We did however identify a strong overlap between genes regulated by the transcription factor, Myc, and AA starvation-responsive genes, particularly those involved in ribosome biogenesis, protein synthesis and mitochondrial function. The consensus Myc DNA binding site is enriched in promoters of these AA starvation genes, and we found that Myc overexpression could bypass dietary AA to induce expression of these genes. We also identified another sequence motif (Motif 1 enriched in the promoters of AA starvation-responsive genes. We showed that Motif 1 was both necessary and sufficient to mediate transcriptional responses to dietary AA in larvae. Conclusions Our data suggest that many of the transcriptional effects of amino acids are mediated via signaling through the TOR pathway in Drosophila larvae. We also find that these transcriptional effects are mediated through at least two mechanisms: via the transcription factor Myc, and via the Motif 1 cis-regulatory element. These studies begin to elucidate a nutrient

  6. Cis-regulatory variants affect CHRNA5 mRNA expression in populations of African and European ancestry.

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    Jen-Chyong Wang

    Full Text Available Variants within the gene cluster encoding α3, α5, and β4 nicotinic receptor subunits are major risk factors for substance dependence. The strongest impact on risk is associated with variation in the CHRNA5 gene, where at least two mechanisms are at work: amino acid variation and altered mRNA expression levels. The risk allele of the non-synonymous variant (rs16969968; D398N primarily occurs on the haplotype containing the low mRNA expression allele. In populations of European ancestry, there are approximately 50 highly correlated variants in the CHRNA5-CHRNA3-CHRNB4 gene cluster and the adjacent PSMA4 gene region that are associated with CHRNA5 mRNA levels. It is not clear which of these variants contribute to the changes in CHRNA5 transcript level. Because populations of African ancestry have reduced linkage disequilibrium among variants spanning this gene cluster, eQTL mapping in subjects of African ancestry could potentially aid in defining the functional variants that affect CHRNA5 mRNA levels. We performed quantitative allele specific gene expression using frontal cortices derived from 49 subjects of African ancestry and 111 subjects of European ancestry. This method measures allele-specific transcript levels in the same individual, which eliminates other biological variation that occurs when comparing expression levels between different samples. This analysis confirmed that substance dependence associated variants have a direct cis-regulatory effect on CHRNA5 transcript levels in human frontal cortices of African and European ancestry and identified 10 highly correlated variants, located in a 9 kb region, that are potential functional variants modifying CHRNA5 mRNA expression levels.

  7. Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs

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    Girgis Hani Z

    2012-02-01

    Full Text Available Abstract Background Researchers seeking to unlock the genetic basis of human physiology and diseases have been studying gene transcription regulation. The temporal and spatial patterns of gene expression are controlled by mainly non-coding elements known as cis-regulatory modules (CRMs and epigenetic factors. CRMs modulating related genes share the regulatory signature which consists of transcription factor (TF binding sites (TFBSs. Identifying such CRMs is a challenging problem due to the prohibitive number of sequence sets that need to be analyzed. Results We formulated the challenge as a supervised classification problem even though experimentally validated CRMs were not required. Our efforts resulted in a software system named CrmMiner. The system mines for CRMs in the vicinity of related genes. CrmMiner requires two sets of sequences: a mixed set and a control set. Sequences in the vicinity of the related genes comprise the mixed set, whereas the control set includes random genomic sequences. CrmMiner assumes that a large percentage of the mixed set is made of background sequences that do not include CRMs. The system identifies pairs of closely located motifs representing vertebrate TFBSs that are enriched in the training mixed set consisting of 50% of the gene loci. In addition, CrmMiner selects a group of the enriched pairs to represent the tissue-specific regulatory signature. The mixed and the control sets are searched for candidate sequences that include any of the selected pairs. Next, an optimal Bayesian classifier is used to distinguish candidates found in the mixed set from their control counterparts. Our study proposes 62 tissue-specific regulatory signatures and putative CRMs for different human tissues and cell types. These signatures consist of assortments of ubiquitously expressed TFs and tissue-specific TFs. Under controlled settings, CrmMiner identified known CRMs in noisy sets up to 1:25 signal-to-noise ratio. CrmMiner was

  8. Conserved cis-regulatory regions in a large genomic landscape control SHH and BMP-regulated Gremlin1 expression in mouse limb buds

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    Zuniga Aimée

    2012-08-01

    Full Text Available Abstract Background Mouse limb bud is a prime model to study the regulatory interactions that control vertebrate organogenesis. Major aspects of limb bud development are controlled by feedback loops that define a self-regulatory signalling system. The SHH/GREM1/AER-FGF feedback loop forms the core of this signalling system that operates between the posterior mesenchymal organiser and the ectodermal signalling centre. The BMP antagonist Gremlin1 (GREM1 is a critical node in this system, whose dynamic expression is controlled by BMP, SHH, and FGF signalling and key to normal progression of limb bud development. Previous analysis identified a distant cis-regulatory landscape within the neighbouring Formin1 (Fmn1 locus that is required for Grem1 expression, reminiscent of the genomic landscapes controlling HoxD and Shh expression in limb buds. Results Three highly conserved regions (HMCO1-3 were identified within the previously defined critical genomic region and tested for their ability to regulate Grem1 expression in mouse limb buds. Using a combination of BAC and conventional transgenic approaches, a 9 kb region located ~70 kb downstream of the Grem1 transcription unit was identified. This region, termed Grem1 Regulatory Sequence 1 (GRS1, is able to recapitulate major aspects of Grem1 expression, as it drives expression of a LacZ reporter into the posterior and, to a lesser extent, in the distal-anterior mesenchyme. Crossing the GRS1 transgene into embryos with alterations in the SHH and BMP pathways established that GRS1 depends on SHH and is modulated by BMP signalling, i.e. integrates inputs from these pathways. Chromatin immunoprecipitation revealed interaction of endogenous GLI3 proteins with the core cis-regulatory elements in the GRS1 region. As GLI3 is a mediator of SHH signal transduction, these results indicated that SHH directly controls Grem1 expression through the GRS1 region. Finally, all cis-regulatory regions within the Grem1

  9. Gene set-based module discovery in the breast cancer transcriptome

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    Zhang Michael Q

    2009-02-01

    Full Text Available Abstract Background Although microarray-based studies have revealed global view of gene expression in cancer cells, we still have little knowledge about regulatory mechanisms underlying the transcriptome. Several computational methods applied to yeast data have recently succeeded in identifying expression modules, which is defined as co-expressed gene sets under common regulatory mechanisms. However, such module discovery methods are not applied cancer transcriptome data. Results In order to decode oncogenic regulatory programs in cancer cells, we developed a novel module discovery method termed EEM by extending a previously reported module discovery method, and applied it to breast cancer expression data. Starting from seed gene sets prepared based on cis-regulatory elements, ChIP-chip data, and gene locus information, EEM identified 10 principal expression modules in breast cancer based on their expression coherence. Moreover, EEM depicted their activity profiles, which predict regulatory programs in each subtypes of breast tumors. For example, our analysis revealed that the expression module regulated by the Polycomb repressive complex 2 (PRC2 is downregulated in triple negative breast cancers, suggesting similarity of transcriptional programs between stem cells and aggressive breast cancer cells. We also found that the activity of the PRC2 expression module is negatively correlated to the expression of EZH2, a component of PRC2 which belongs to the E2F expression module. E2F-driven EZH2 overexpression may be responsible for the repression of the PRC2 expression modules in triple negative tumors. Furthermore, our network analysis predicts regulatory circuits in breast cancer cells. Conclusion These results demonstrate that the gene set-based module discovery approach is a powerful tool to decode regulatory programs in cancer cells.

  10. A Generalized Linear Model for Decomposing Cis-regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression

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    Yasuaki Takada

    2017-07-01

    Full Text Available Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory (i.e., allelic genotype, genomic imprinting [i.e., parent-of-origin (PO], and maternal [i.e., maternal genotype (MG] effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, whereas more genes with significant MG effect were observed in livers. Further application of this method will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.

  11. Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic.

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    Ah-Ram Kim

    Full Text Available Rearrangements of about 2.5 kilobases of regulatory DNA located 5' of the transcription start site of the Drosophila even-skipped locus generate large-scale changes in the expression of even-skipped stripes 2, 3, and 7. The most radical effects are generated by juxtaposing the minimal stripe enhancers MSE2 and MSE3 for stripes 2 and 3 with and without small "spacer" segments less than 360 bp in length. We placed these fusion constructs in a targeted transformation site and obtained quantitative expression data for these transformants together with their controlling transcription factors at cellular resolution. These data demonstrated that the rearrangements can alter expression levels in stripe 2 and the 2-3 interstripe by a factor of more than 10. We reasoned that this behavior would place tight constraints on possible rules of genomic cis-regulatory logic. To find these constraints, we confronted our new expression data together with previously obtained data on other constructs with a computational model. The model contained representations of thermodynamic protein-DNA interactions including steric interference and cooperative binding, short-range repression, direct repression, activation, and coactivation. The model was highly constrained by the training data, which it described within the limits of experimental error. The model, so constrained, was able to correctly predict expression patterns driven by enhancers for other Drosophila genes; even-skipped enhancers not included in the training set; stripe 2, 3, and 7 enhancers from various Drosophilid and Sepsid species; and long segments of even-skipped regulatory DNA that contain multiple enhancers. The model further demonstrated that elevated expression driven by a fusion of MSE2 and MSE3 was a consequence of the recruitment of a portion of MSE3 to become a functional component of MSE2, demonstrating that cis-regulatory "elements" are not elementary objects.

  12. The contribution of cis-regulatory elements to head-to-head gene pairs’ co-expression pattern

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Transcription regulation is one of the most critical pipelines in biological process,in which cis-elements play the role as gene expression regulators.We attempt to deduce the principles underlying the co-expression of "head-to-head" gene pairs by analyzing activities or behaviors of the shared cis-elements.A network component analysis was performed to estimate the impact of cis-elements on gene promoters and their activities under different conditions.Our discoveries reveal how biological system uses those regulatory elements to control the expression pattern of "head-to-head" gene pairs and the whole transcription regulation system.

  13. TP Decoding

    CERN Document Server

    Lu, Yi; Montanari, Andrea

    2007-01-01

    'Tree pruning' (TP) is an algorithm for probabilistic inference on binary Markov random fields. It has been recently derived by Dror Weitz and used to construct the first fully polynomial approximation scheme for counting independent sets up to the `tree uniqueness threshold.' It can be regarded as a clever method for pruning the belief propagation computation tree, in such a way to exactly account for the effect of loops. In this paper we generalize the original algorithm to make it suitable for decoding linear codes, and discuss various schemes for pruning the computation tree. Further, we present the outcomes of numerical simulations on several linear codes, showing that tree pruning allows to interpolate continuously between belief propagation and maximum a posteriori decoding. Finally, we discuss theoretical implications of the new method.

  14. Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs.

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    Christopher D Brown

    Full Text Available Genetic variants in cis-regulatory elements or trans-acting regulators frequently influence the quantity and spatiotemporal distribution of gene transcription. Recent interest in expression quantitative trait locus (eQTL mapping has paralleled the adoption of genome-wide association studies (GWAS for the analysis of complex traits and disease in humans. Under the hypothesis that many GWAS associations tag non-coding SNPs with small effects, and that these SNPs exert phenotypic control by modifying gene expression, it has become common to interpret GWAS associations using eQTL data. To fully exploit the mechanistic interpretability of eQTL-GWAS comparisons, an improved understanding of the genetic architecture and causal mechanisms of cell type specificity of eQTLs is required. We address this need by performing an eQTL analysis in three parts: first we identified eQTLs from eleven studies on seven cell types; then we integrated eQTL data with cis-regulatory element (CRE data from the ENCODE project; finally we built a set of classifiers to predict the cell type specificity of eQTLs. The cell type specificity of eQTLs is associated with eQTL SNP overlap with hundreds of cell type specific CRE classes, including enhancer, promoter, and repressive chromatin marks, regions of open chromatin, and many classes of DNA binding proteins. These associations provide insight into the molecular mechanisms generating the cell type specificity of eQTLs and the mode of regulation of corresponding eQTLs. Using a random forest classifier with cell specific CRE-SNP overlap as features, we demonstrate the feasibility of predicting the cell type specificity of eQTLs. We then demonstrate that CREs from a trait-associated cell type can be used to annotate GWAS associations in the absence of eQTL data for that cell type. We anticipate that such integrative, predictive modeling of cell specificity will improve our ability to understand the mechanistic basis of human

  15. A cis-regulatory mutation in troponin-I of Drosophila reveals the importance of proper stoichiometry of structural proteins during muscle assembly.

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    Firdaus, Hena; Mohan, Jayaram; Naz, Sarwat; Arathi, Prabhashankar; Ramesh, Saraf R; Nongthomba, Upendra

    2015-05-01

    Rapid and high wing-beat frequencies achieved during insect flight are powered by the indirect flight muscles, the largest group of muscles present in the thorax. Any anomaly during the assembly and/or structural impairment of the indirect flight muscles gives rise to a flightless phenotype. Multiple mutagenesis screens in Drosophila melanogaster for defective flight behavior have led to the isolation and characterization of mutations that have been instrumental in the identification of many proteins and residues that are important for muscle assembly, function, and disease. In this article, we present a molecular-genetic characterization of a flightless mutation, flightless-H (fliH), originally designated as heldup-a (hdp-a). We show that fliH is a cis-regulatory mutation of the wings up A (wupA) gene, which codes for the troponin-I protein, one of the troponin complex proteins, involved in regulation of muscle contraction. The mutation leads to reduced levels of troponin-I transcript and protein. In addition to this, there is also coordinated reduction in transcript and protein levels of other structural protein isoforms that are part of the troponin complex. The altered transcript and protein stoichiometry ultimately culminates in unregulated acto-myosin interactions and a hypercontraction muscle phenotype. Our results shed new insights into the importance of maintaining the stoichiometry of structural proteins during muscle assembly for proper function with implications for the identification of mutations and disease phenotypes in other species, including humans.

  16. Combining computational prediction of cis-regulatory elements with a new enhancer assay to efficiently label neuronal structures in the medaka fish.

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    Emmanuel Mongin

    Full Text Available The developing vertebrate nervous system contains a remarkable array of neural cells organized into complex, evolutionarily conserved structures. The labeling of living cells in these structures is key for the understanding of brain development and function, yet the generation of stable lines expressing reporter genes in specific spatio-temporal patterns remains a limiting step. In this study we present a fast and reliable pipeline to efficiently generate a set of stable lines expressing a reporter gene in multiple neuronal structures in the developing nervous system in medaka. The pipeline combines both the accurate computational genome-wide prediction of neuronal specific cis-regulatory modules (CRMs and a newly developed experimental setup to rapidly obtain transgenic lines in a cost-effective and highly reproducible manner. 95% of the CRMs tested in our experimental setup show enhancer activity in various and numerous neuronal structures belonging to all major brain subdivisions. This pipeline represents a significant step towards the dissection of embryonic neuronal development in vertebrates.

  17. Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules

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    Roytberg Mikhail A

    2007-10-01

    Full Text Available Abstract Background cis-Regulatory modules (CRMs of eukaryotic genes often contain multiple binding sites for transcription factors. The phenomenon that binding sites form clusters in CRMs is exploited in many algorithms to locate CRMs in a genome. This gives rise to the problem of calculating the statistical significance of the event that multiple sites, recognized by different factors, would be found simultaneously in a text of a fixed length. The main difficulty comes from overlapping occurrences of motifs. So far, no tools have been developed allowing the computation of p-values for simultaneous occurrences of different motifs which can overlap. Results We developed and implemented an algorithm computing the p-value that s different motifs occur respectively k1, ..., ks or more times, possibly overlapping, in a random text. Motifs can be represented with a majority of popular motif models, but in all cases, without indels. Zero or first order Markov chains can be adopted as a model for the random text. The computational tool was tested on the set of cis-regulatory modules involved in D. melanogaster early development, for which there exists an annotation of binding sites for transcription factors. Our test allowed us to correctly identify transcription factors cooperatively/competitively binding to DNA. Method The algorithm that precisely computes the probability of simultaneous motif occurrences is inspired by the Aho-Corasick automaton and employs a prefix tree together with a transition function. The algorithm runs with the O(n|Σ|(m|ℋ MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaat0uy0HwzTfgDPnwy1egaryqtHrhAL1wy0L2yHvdaiqaacqWFlecsaaa@3762@| + K|σ|K ∏i ki time complexity, where n is the length of the text, |Σ| is the alphabet size, m is the

  18. PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups

    Directory of Open Access Journals (Sweden)

    Huang Hsien-Da

    2008-11-01

    Full Text Available Abstract Background The elucidation of transcriptional regulation in plant genes is important area of research for plant scientists, following the mapping of various plant genomes, such as A. thaliana, O. sativa and Z. mays. A variety of bioinformatic servers or databases of plant promoters have been established, although most have been focused only on annotating transcription factor binding sites in a single gene and have neglected some important regulatory elements (tandem repeats and CpG/CpNpG islands in promoter regions. Additionally, the combinatorial interaction of transcription factors (TFs is important in regulating the gene group that is associated with the same expression pattern. Therefore, a tool for detecting the co-regulation of transcription factors in a group of gene promoters is required. Results This study develops a database-assisted system, PlantPAN (Plant Promoter Analysis Navigator, for recognizing combinatorial cis-regulatory elements with a distance constraint in sets of plant genes. The system collects the plant transcription factor binding profiles from PLACE, TRANSFAC (public release 7.0, AGRIS, and JASPER databases and allows users to input a group of gene IDs or promoter sequences, enabling the co-occurrence of combinatorial transcription factor binding sites (TFBSs within a defined distance (20 bp to 200 bp to be identified. Furthermore, the new resource enables other regulatory features in a plant promoter, such as CpG/CpNpG islands and tandem repeats, to be displayed. The regulatory elements in the conserved regions of the promoters across homologous genes are detected and presented. Conclusion In addition to providing a user-friendly input/output interface, PlantPAN has numerous advantages in the analysis of a plant promoter. Several case studies have established the effectiveness of PlantPAN. This novel analytical resource is now freely available at http://PlantPAN.mbc.nctu.edu.tw.

  19. Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.

    Science.gov (United States)

    Kang, Keunsoo; Kim, Joomyeong; Chung, Jae Hoon; Lee, Daeyoup

    2011-09-01

    The identification of genome-wide cis-regulatory modules (CRMs) and characterization of their associated epigenetic features are fundamental steps toward the understanding of gene regulatory networks. Although integrative analysis of available genome-wide information can provide new biological insights, the lack of novel methodologies has become a major bottleneck. Here, we present a comprehensive analysis tool called combinatorial CRM decoder (CCD), which utilizes the publicly available information to identify and characterize genome-wide CRMs in a species of interest. CCD first defines a set of the epigenetic features which is significantly associated with a set of known CRMs as a code called 'trace code', and subsequently uses the trace code to pinpoint putative CRMs throughout the genome. Using 61 genome-wide data sets obtained from 17 independent mouse studies, CCD successfully catalogued ∼12 600 CRMs (five distinct classes) including polycomb repressive complex 2 target sites as well as imprinting control regions. Interestingly, we discovered that ∼4% of the identified CRMs belong to at least two different classes named 'multi-functional CRM', suggesting their functional importance for regulating spatiotemporal gene expression. From these examples, we show that CCD can be applied to any potential genome-wide datasets and therefore will shed light on unveiling genome-wide CRMs in various species.

  20. Deletion hotspots in AMACR promoter CpG island are cis-regulatory elements controlling the gene expression in the colon.

    Directory of Open Access Journals (Sweden)

    Xiang Zhang

    2009-01-01

    Full Text Available Alpha-methylacyl-coenzyme A racemase (AMACR regulates peroxisomal beta-oxidation of phytol-derived, branched-chain fatty acids from red meat and dairy products -- suspected risk factors for colon carcinoma (CCa. AMACR was first found overexpressed in prostate cancer but not in benign glands and is now an established diagnostic marker for prostate cancer. Aberrant expression of AMACR was recently reported in Cca; however, little is known about how this gene is abnormally activated in cancer. By using a panel of immunostained-laser-capture-microdissected clinical samples comprising the entire colon adenoma-carcinoma sequence, we show that deregulation of AMACR during colon carcinogenesis involves two nonrandom events, resulting in the mutually exclusive existence of double-deletion at CG3 and CG10 and deletion of CG12-16 in a newly identified CpG island within the core promoter of AMACR. The double-deletion at CG3 and CG10 was found to be a somatic lesion. It existed in histologically normal colonic glands and tubular adenomas with low AMACR expression and was absent in villous adenomas and all CCas expressing variable levels of AMACR. In contrast, deletion of CG12-16 was shown to be a constitutional allele with a frequency of 43% in a general population. Its prevalence reached 89% in moderately differentiated CCas strongly expressing AMACR but only existed at 14% in poorly differentiated CCas expressing little or no AMACR. The DNA sequences housing these deletions were found to be putative cis-regulatory elements for Sp1 at CG3 and CG10, and ZNF202 at CG12-16. Chromatin immunoprecipitation, siRNA knockdown, gel shift assay, ectopic expression, and promoter analyses supported the regulation by Sp1 and ZNF202 of AMACR gene expression in an opposite manner. Our findings identified key in vivo events and novel transcription factors responsible for AMACR regulation in CCas and suggested these AMACR deletions may have diagnostic/prognostic value for

  1. Iterative List Decoding

    DEFF Research Database (Denmark)

    Justesen, Jørn; Høholdt, Tom; Hjaltason, Johan

    2005-01-01

    We analyze the relation between iterative decoding and the extended parity check matrix. By considering a modified version of bit flipping, which produces a list of decoded words, we derive several relations between decodable error patterns and the parameters of the code. By developing a tree...... of codewords at minimal distance from the received vector, we also obtain new information about the code....

  2. Preaxial polydactyly/triphalangeal thumb is associated with changed transcription factor-binding affinity in a family with a novel point mutation in the long-range cis-regulatory element ZRS

    DEFF Research Database (Denmark)

    Farooq, Muhammad; Troelsen, Jesper T; Boyd, Mette

    2010-01-01

    have been reported in ZRS, the underlying regulatory mechanism is still unknown. In this study, we analyzed the effect on transcription factor binding of a novel ZRS point mutation (463T>G) in a Pakistani family with preaxial polydactyly and triphalangeal thumb. Electrophoretical mobility shift assay......A cis-regulatory sequence also known as zone of polarizing activity (ZPA) regulatory sequence (ZRS) located in intron 5 of LMBR1 is essential for expression of sonic hedgehog (SHH) in the developing posterior limb bud mesenchyme. Even though many point mutations causing preaxial duplication defects...

  3. Forced Sequence Sequential Decoding

    DEFF Research Database (Denmark)

    Jensen, Ole Riis

    In this thesis we describe a new concatenated decoding scheme based on iterations between an inner sequentially decoded convolutional code of rate R=1/4 and memory M=23, and block interleaved outer Reed-Solomon codes with non-uniform profile. With this scheme decoding with good performance is pos...... of computational overflow. Analytical results for the probability that the first Reed-Solomon word is decoded after C computations are presented. This is supported by simulation results that are also extended to other parameters....

  4. High Speed Viterbi Decoder Architecture

    DEFF Research Database (Denmark)

    Paaske, Erik; Andersen, Jakob Dahl

    1998-01-01

    The fastest commercially available Viterbi decoders for the (171,133) standard rate 1/2 code operate with a decoding speed of 40-50 Mbit/s (net data rate). In this paper we present a suitable architecture for decoders operating with decoding speeds of 150-300 Mbit/s.......The fastest commercially available Viterbi decoders for the (171,133) standard rate 1/2 code operate with a decoding speed of 40-50 Mbit/s (net data rate). In this paper we present a suitable architecture for decoders operating with decoding speeds of 150-300 Mbit/s....

  5. Forced Sequence Sequential Decoding

    DEFF Research Database (Denmark)

    Jensen, Ole Riis; Paaske, Erik

    1998-01-01

    the iteration process provides the sequential decoders with side information that allows a smaller average load and minimizes the probability of computational overflow. Analytical results for the probability that the first RS word is decoded after C computations are presented. These results are supported...

  6. JSATS Decoder Software Manual

    Energy Technology Data Exchange (ETDEWEB)

    Flory, Adam E.; Lamarche, Brian L.; Weiland, Mark A.

    2013-05-01

    The Juvenile Salmon Acoustic Telemetry System (JSATS) Decoder is a software application that converts a digitized acoustic signal (a waveform stored in the .bwm file format) into a list of potential JSATS Acoustic MicroTransmitter (AMT) tagcodes along with other data about the signal including time of arrival and signal to noise ratios (SNR). This software is capable of decoding single files, directories, and viewing raw acoustic waveforms. When coupled with the JSATS Detector, the Decoder is capable of decoding in ‘real-time’ and can also provide statistical information about acoustic beacons placed within receive range of hydrophones within a JSATS array. This document details the features and functionality of the software. The document begins with software installation instructions (section 2), followed in order by instructions for decoder setup (section 3), decoding process initiation (section 4), then monitoring of beacons (section 5) using real-time decoding features. The last section in the manual describes the beacon, beacon statistics, and the results file formats. This document does not consider the raw binary waveform file format.

  7. Decoding Astronomical Concepts

    Science.gov (United States)

    Durisen, Richard H.; Pilachowski, Catherine A.

    2004-01-01

    Two astronomy professors, using the Decoding the Disciplines process, help their students use abstract theories to analyze light and to visualize the enormous scale of astronomical concepts. (Contains 5 figures.)

  8. Optimization of MPEG decoding

    DEFF Research Database (Denmark)

    Martins, Bo; Forchhammer, Søren

    1999-01-01

    MPEG-2 video decoding is examined. A unified approach to quality improvement, chrominance upsampling, de-interlacing and superresolution is presented. The information over several frames is combined as part of the processing.......MPEG-2 video decoding is examined. A unified approach to quality improvement, chrominance upsampling, de-interlacing and superresolution is presented. The information over several frames is combined as part of the processing....

  9. List Decoding of Algebraic Codes

    DEFF Research Database (Denmark)

    Nielsen, Johan Sebastian Rosenkilde

    We investigate three paradigms for polynomial-time decoding of Reed–Solomon codes beyond half the minimum distance: the Guruswami–Sudan algorithm, Power decoding and the Wu algorithm. The main results concern shaping the computational core of all three methods to a problem solvable by module...... give: a fast maximum-likelihood list decoder based on the Guruswami–Sudan algorithm; a new variant of Power decoding, Power Gao, along with some new insights into Power decoding; and a new, module based method for performing rational interpolation for theWu algorithm. We also show how to decode...

  10. Interpretability in Linear Brain Decoding

    OpenAIRE

    Kia, Seyed Mostafa; Passerini, Andrea

    2016-01-01

    Improving the interpretability of brain decoding approaches is of primary interest in many neuroimaging studies. Despite extensive studies of this type, at present, there is no formal definition for interpretability of brain decoding models. As a consequence, there is no quantitative measure for evaluating the interpretability of different brain decoding methods. In this paper, we present a simple definition for interpretability of linear brain decoding models. Then, we propose to combine the...

  11. Decoding Xing-Ling codes

    DEFF Research Database (Denmark)

    Nielsen, Rasmus Refslund

    2002-01-01

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

  12. Decoding Children's Expressions of Affect.

    Science.gov (United States)

    Feinman, Joel A.; Feldman, Robert S.

    Mothers' ability to decode the emotional expressions of their male and female children was compared to the decoding ability of non-mothers. Happiness, sadness, fear and anger were induced in children in situations that varied in terms of spontaneous and role-played encoding modes. It was hypothesized that mothers would be more accurate decoders of…

  13. A universal algorithm for genome-wide in silicio identification of biologically significant gene promoter putative cis-regulatory-elements; identification of new elements for reactive oxygen species and sucrose signaling in Arabidopsis.

    Science.gov (United States)

    Geisler, Matt; Kleczkowski, Leszek A; Karpinski, Stanislaw

    2006-02-01

    Short motifs of many cis-regulatory elements (CREs) can be found in the promoters of most Arabidopsis genes, and this raises the question of how their presence can confer specific regulation. We developed a universal algorithm to test the biological significance of CREs by first identifying every Arabidopsis gene with a CRE and then statistically correlating the presence or absence of the element with the gene expression profile on multiple DNA microarrays. This algorithm was successfully verified for previously characterized abscisic acid, ethylene, sucrose and drought responsive CREs in Arabidopsis, showing that the presence of these elements indeed correlates with treatment-specific gene induction. Later, we used standard motif sampling methods to identify 128 putative motifs induced by excess light, reactive oxygen species and sucrose. Our algorithm was able to filter 20 out of 128 novel CREs which significantly correlated with gene induction by either heat, reactive oxygen species and/or sucrose. The position, orientation and sequence specificity of CREs was tested in silicio by analyzing the expression of genes with naturally occurring sequence variations. In three novel CREs the forward orientation correlated with sucrose induction and the reverse orientation with sucrose suppression. The functionality of the predicted novel CREs was experimentally confirmed using Arabidopsis cell-suspension cultures transformed with short promoter fragments or artificial promoters fused with the GUS reporter gene. Our genome-wide analysis opens up new possibilities for in silicio verification of the biological significance of newly discovered CREs, and allows for subsequent selection of such CREs for experimental studies.

  14. Gene expression profiling of cultured human NF1 heterozygous (NF1+/-) melanocytes reveals downregulation of a transcriptional cis-regulatory network mediating activation of the melanocyte-specific dopachrome tautomerase (DCT) gene.

    Science.gov (United States)

    Boucneau, Joachim; De Schepper, Sofie; Vuylsteke, Marnik; Van Hummelen, Paul; Naeyaert, Jean-Marie; Lambert, Jo

    2005-08-01

    One of the major primary features of the neurocutaneous genetic disorder Neurofibromatosis type 1 are the hyperpigmentary café-au-lait macules where disregulation of melanocyte biology is supposed to play a key etiopathogenic role. To gain better insight into the possible role of the tumor suppressor gene NF1, a transcriptomic microarray analysis was performed on human NF1 heterozygous (NF1+/-) melanocytes of a Neurofibromatosis type 1 patient and NF1 wild type (NF1+/+) melanocytes of a healthy control patient, both cultured from normally pigmented skin and hyperpigmented lesional café-au-lait skin. From the magnitude of gene effects, we found that gene expression was affected most strongly by genotype and less so by lesional type. A total of 137 genes had a significant twofold or more up- (72) or downregulated (65) expression in NF1+/- melanocytes compared with NF1+/+ melanocytes. Melanocytes cultured from hyperpigmented café-au-lait skin showed 37 upregulated genes whereas only 14 were downregulated compared with normal skin melanocytes. In addition, significant genotype xlesional type interactions were observed for 465 genes. Differentially expressed genes were mainly involved in regulating cell proliferation and cell adhesion. A high number of transcription factor genes, among which a specific subset important in melanocyte lineage development, were downregulated in the cis-regulatory network governing the activation of the melanocyte-specific dopachrome tautomerase (DCT) gene. Although the results presented have been obtained with a restricted number of patients (one NF1 patient and one control) and using cDNA microarrays that may limit their interpretation, the data nevertheless addresses for the first time the effect of a heterozygous NF1 gene on the expression of the human melanocyte transcriptome and has generated several interesting candidate genes helpful in elucidating the etiopathology of café-au-lait macules in NF1 patients.

  15. Coding and decoding with dendrites.

    Science.gov (United States)

    Papoutsi, Athanasia; Kastellakis, George; Psarrou, Maria; Anastasakis, Stelios; Poirazi, Panayiota

    2014-02-01

    Since the discovery of complex, voltage dependent mechanisms in the dendrites of multiple neuron types, great effort has been devoted in search of a direct link between dendritic properties and specific neuronal functions. Over the last few years, new experimental techniques have allowed the visualization and probing of dendritic anatomy, plasticity and integrative schemes with unprecedented detail. This vast amount of information has caused a paradigm shift in the study of memory, one of the most important pursuits in Neuroscience, and calls for the development of novel theories and models that will unify the available data according to some basic principles. Traditional models of memory considered neural cells as the fundamental processing units in the brain. Recent studies however are proposing new theories in which memory is not only formed by modifying the synaptic connections between neurons, but also by modifications of intrinsic and anatomical dendritic properties as well as fine tuning of the wiring diagram. In this review paper we present previous studies along with recent findings from our group that support a key role of dendrites in information processing, including the encoding and decoding of new memories, both at the single cell and the network level. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Academic Training - Bioinformatics: Decoding the Genome

    CERN Multimedia

    Chris Jones

    2006-01-01

    ACADEMIC TRAINING LECTURE SERIES 27, 28 February 1, 2, 3 March 2006 from 11:00 to 12:00 - Auditorium, bldg. 500 Decoding the Genome A special series of 5 lectures on: Recent extraordinary advances in the life sciences arising through new detection technologies and bioinformatics The past five years have seen an extraordinary change in the information and tools available in the life sciences. The sequencing of the human genome, the discovery that we possess far fewer genes than foreseen, the measurement of the tiny changes in the genomes that differentiate us, the sequencing of the genomes of many pathogens that lead to diseases such as malaria are all examples of completely new information that is now available in the quest for improved healthcare. New tools have allowed similar strides in the discovery of the associated protein structures, providing invaluable information for those searching for new drugs. New DNA microarray chips permit simultaneous measurement of the state of expression of tens...

  17. Loneliness and Interpersonal Decoding Skills.

    Science.gov (United States)

    Zakahi, Walter R.; Goss, Blaine

    1995-01-01

    Finds that the romantic loneliness dimension of the Differential Loneliness Scale is related to decoding ability, and that there are moderate linear relationships among several of the dimensions of the Differential Loneliness Scale, the self-report of listening ability, and participants' view of their own decoding ability. (SR)

  18. Assessment of composite motif discovery methods

    Directory of Open Access Journals (Sweden)

    Johansen Jostein

    2008-02-01

    Full Text Available Abstract Background Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have addressed the problem of single motif discovery – discovering binding motifs for individual transcription factors. In higher organisms, however, transcription factors usually act in combination with nearby bound factors to induce specific regulatory behaviours. Hence, recent focus has shifted from single motifs to the discovery of sets of motifs bound by multiple cooperating transcription factors, so called composite motifs or cis-regulatory modules. Given the large number and diversity of methods available, independent assessment of methods becomes important. Although there have been several benchmark studies of single motif discovery, no similar studies have previously been conducted concerning composite motif discovery. Results We have developed a benchmarking framework for composite motif discovery and used it to evaluate the performance of eight published module discovery tools. Benchmark datasets were constructed based on real genomic sequences containing experimentally verified regulatory modules, and the module discovery programs were asked to predict both the locations of these modules and to specify the single motifs involved. To aid the programs in their search, we provided position weight matrices corresponding to the binding motifs of the transcription factors involved. In addition, selections of decoy matrices were mixed with the genuine matrices on one dataset to test the response of programs to varying levels of noise. Conclusion Although some of the methods tested tended to score somewhat better than others overall, there were still large variations between individual datasets and no single method performed consistently better than the rest in all situations. The variation in performance on individual

  19. The Formal Specifications for Protocols of Decoders

    Institute of Scientific and Technical Information of China (English)

    YUAN Meng-ting; WU Guo-qing; SHU Feng-di

    2004-01-01

    This paper presents a formal approach, FSPD (Formal Specifications for Protocols of Decoders), to specify decoder communication protocols. Based on axiomatic, FSPD is a precise language with which programmers could use only one suitable driver to handle various types of decoders. FSPD is helpful for programmers to get high adaptability and reusability of decoder-driver software.

  20. Astrophysics Decoding the cosmos

    CERN Document Server

    Irwin, Judith A

    2007-01-01

    Astrophysics: Decoding the Cosmos is an accessible introduction to the key principles and theories underlying astrophysics. This text takes a close look at the radiation and particles that we receive from astronomical objects, providing a thorough understanding of what this tells us, drawing the information together using examples to illustrate the process of astrophysics. Chapters dedicated to objects showing complex processes are written in an accessible manner and pull relevant background information together to put the subject firmly into context. The intention of the author is that the book will be a 'tool chest' for undergraduate astronomers wanting to know the how of astrophysics. Students will gain a thorough grasp of the key principles, ensuring that this often-difficult subject becomes more accessible.

  1. Decoding the productivity code

    DEFF Research Database (Denmark)

    Hansen, David

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

  2. Neural Decoder for Topological Codes

    Science.gov (United States)

    Torlai, Giacomo; Melko, Roger G.

    2017-07-01

    We present an algorithm for error correction in topological codes that exploits modern machine learning techniques. Our decoder is constructed from a stochastic neural network called a Boltzmann machine, of the type extensively used in deep learning. We provide a general prescription for the training of the network and a decoding strategy that is applicable to a wide variety of stabilizer codes with very little specialization. We demonstrate the neural decoder numerically on the well-known two-dimensional toric code with phase-flip errors.

  3. Decoding by Embedding: Correct Decoding Radius and DMT Optimality

    CERN Document Server

    Ling, Cong; Luzzi, Laura; Stehle, Damien

    2011-01-01

    In lattice-coded multiple-input multiple-output (MIMO) systems, optimal decoding amounts to solving the closest vector problem (CVP). Embedding is a powerful technique for the approximate CVP, yet its remarkable performance is not well understood. In this paper, we analyze the embedding technique from a bounded distance decoding (BDD) viewpoint. We prove that the Lenstra, Lenstra and Lov\\'az (LLL) algorithm can achieve 1/(2{\\gamma}) -BDD for {\\gamma} \\approx O(2^(n/4)), yielding a polynomial-complexity decoding algorithm performing exponentially better than Babai's which achieves {\\gamma} = O(2^(n/2)). This substantially improves the existing result {\\gamma} = O(2^(n)) for embedding decoding. We also prove that BDD of the regularized lattice is optimal in terms of the diversity-multiplexing gain tradeoff (DMT).

  4. Decoding OvTDM with sphere-decoding algorithm

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Overlapped time division multiplexing (OvTDM) is a new type of transmission scheme with high spectrum efficiency and low threshold signal-to-noise ratio (SNR). In this article, the structure of OvTDM is introduced and the sphere-decoding algorithm of complex domain is proposed for OvTDM. Simulations demonstrate that the proposed algorithm can achieve maximum likelihood (ML) decoding with lower complexity as compared to traditional maximum likelihood sequence demodulation (MLSD) or viterbi algorithm (VA).

  5. Decode the Sodium Label Lingo

    Science.gov (United States)

    ... For Preschooler For Gradeschooler For Teen Decode the Sodium Label Lingo Published January 24, 2013 Print Email Reading food labels can help you slash sodium. Here's how to decipher them. "Sodium free" or " ...

  6. Pipelined Viterbi Decoder Using FPGA

    Directory of Open Access Journals (Sweden)

    Nayel Al-Zubi

    2013-02-01

    Full Text Available Convolutional encoding is used in almost all digital communication systems to get better gain in BER (Bit Error Rate, and all applications needs high throughput rate. The Viterbi algorithm is the solution in decoding process. The nonlinear and feedback nature of the Viterbi decoder makes its high speed implementation harder. One of promising approaches to get high throughput in the Viterbi decoder is to introduce a pipelining. This work applies a carry-save technique, which gets the advantage that the critical path in the ACS feedback becomes in one direction and get rid of carry ripple in the “Add” part of ACS unit. In this simulation and implementation show how this technique will improve the throughput of the Viterbi decoder. The design complexities for the bit-pipelined architecture are evaluated and demonstrated using Verilog HDL simulation. And a general algorithm in software that simulates a Viterbi Decoder was developed. Our research is concerned with implementation of the Viterbi Decoders for Field Programmable Gate Arrays (FPGA. Generally FPGA's are slower than custom integrated circuits but can be configured in the lab in few hours as compared to fabrication which takes few months. The design implemented using Verilog HDL and synthesized for Xilinx FPGA's.

  7. Orientation decoding: Sense in spirals?

    Science.gov (United States)

    Clifford, Colin W G; Mannion, Damien J

    2015-04-15

    The orientation of a visual stimulus can be successfully decoded from the multivariate pattern of fMRI activity in human visual cortex. Whether this capacity requires coarse-scale orientation biases is controversial. We and others have advocated the use of spiral stimuli to eliminate a potential coarse-scale bias-the radial bias toward local orientations that are collinear with the centre of gaze-and hence narrow down the potential coarse-scale biases that could contribute to orientation decoding. The usefulness of this strategy is challenged by the computational simulations of Carlson (2014), who reported the ability to successfully decode spirals of opposite sense (opening clockwise or counter-clockwise) from the pooled output of purportedly unbiased orientation filters. Here, we elaborate the mathematical relationship between spirals of opposite sense to confirm that they cannot be discriminated on the basis of the pooled output of unbiased or radially biased orientation filters. We then demonstrate that Carlson's (2014) reported decoding ability is consistent with the presence of inadvertent biases in the set of orientation filters; biases introduced by their digital implementation and unrelated to the brain's processing of orientation. These analyses demonstrate that spirals must be processed with an orientation bias other than the radial bias for successful decoding of spiral sense.

  8. Decoding Dyslexia, a Common Learning Disability

    Science.gov (United States)

    ... of this page please turn JavaScript on. Feature: Dyslexia Decoding Dyslexia, a Common Learning Disability Past Issues / Winter 2016 ... Dyslexic" Articles In Their Own Words: Dealing with Dyslexia / Decoding Dyslexia, a Common Learning Disability / What is ...

  9. Decoding, Semantic Processing, and Reading Comprehension Skill

    Science.gov (United States)

    Golinkoff, Roberta Michnick; Rosinski, Richard R.

    1976-01-01

    A set of decoding tests and picture-word interference tasks was administered to third and fifth graders to explore the relationship between single-word decoding, single-word semantic processing, and text comprehension skill. (BRT)

  10. Modular VLSI Reed-Solomon Decoder

    Science.gov (United States)

    Hsu, In-Shek; Truong, Trieu-Kie

    1991-01-01

    Proposed Reed-Solomon decoder contains multiple very-large-scale integrated (VLSI) circuit chips of same type. Each chip contains sets of logic cells and subcells performing functions from all stages of decoding process. Full decoder assembled by concatenating chips, with selective utilization of cells in particular chips. Cost of development reduced by factor of 5. In addition, decoder programmable in field and switched between 8-bit and 10-bit symbol sizes.

  11. Modular VLSI Reed-Solomon Decoder

    Science.gov (United States)

    Hsu, In-Shek; Truong, Trieu-Kie

    1991-01-01

    Proposed Reed-Solomon decoder contains multiple very-large-scale integrated (VLSI) circuit chips of same type. Each chip contains sets of logic cells and subcells performing functions from all stages of decoding process. Full decoder assembled by concatenating chips, with selective utilization of cells in particular chips. Cost of development reduced by factor of 5. In addition, decoder programmable in field and switched between 8-bit and 10-bit symbol sizes.

  12. Interference Decoding for Deterministic Channels

    CERN Document Server

    Bandemer, Bernd

    2010-01-01

    An inner bound to the capacity region of a class of three user pair deterministic interference channels is presented. The key idea is to simultaneously decode the combined interference signal and the intended message at each receiver. It is shown that this interference decoding inner bound is strictly larger than the inner bound obtained by treating interference as noise, which includes interference alignment for deterministic channels. The gain comes from judicious analysis of the number of combined interference sequences in different regimes of input distributions and message rates.

  13. FPGA Realization of Memory 10 Viterbi Decoder

    DEFF Research Database (Denmark)

    Paaske, Erik; Bach, Thomas Bo; Andersen, Jakob Dahl

    1997-01-01

    sequence mode when feedback from the Reed-Solomon decoder is available. The Viterbi decoder is realized using two Altera FLEX 10K50 FPGA's. The overall operating speed is 30 kbit/s, and since up to three iterations are performed for each frame and only one decoder is used, the operating speed...

  14. Soft-decision decoding of RS codes

    DEFF Research Database (Denmark)

    Justesen, Jørn

    2005-01-01

    By introducing a few simplifying assumptions we derive a simple condition for successful decoding using the Koetter-Vardy algorithm for soft-decision decoding of RS codes. We show that the algorithm has a significant advantage over hard decision decoding when the code rate is low, when two or more...

  15. TURBO DECODER USING LOCAL SUBSIDIARY MAXIMUM LIKELIHOOD DECODING IN PRIOR ESTIMATION OF THE EXTRINSIC INFORMATION

    Institute of Scientific and Technical Information of China (English)

    Yang Fengfan

    2004-01-01

    A new technique for turbo decoder is proposed by using a local subsidiary maximum likelihood decoding and a probability distributions family for the extrinsic information. The optimal distribution of the extrinsic information is dynamically specified for each component decoder.The simulation results show that the iterative decoder with the new technique outperforms that of the decoder with the traditional Gaussian approach for the extrinsic information under the same conditions.

  16. Behavioral approach to list decoding

    NARCIS (Netherlands)

    Polderman, Jan Willem; Kuijper, Margreta

    2002-01-01

    List decoding may be translated into a bivariate interpolation problem. The interpolation problem is to find a bivariate polynomial of minimal weighted degree that interpolates a given set of pairs taken from a finite field. We present a behavioral approach to this interpolation problem. With the da

  17. Decoding intention at sensorimotor timescales.

    Directory of Open Access Journals (Sweden)

    Mathew Salvaris

    Full Text Available The ability to decode an individual's intentions in real time has long been a 'holy grail' of research on human volition. For example, a reliable method could be used to improve scientific study of voluntary action by allowing external probe stimuli to be delivered at different moments during development of intention and action. Several Brain Computer Interface applications have used motor imagery of repetitive actions to achieve this goal. These systems are relatively successful, but only if the intention is sustained over a period of several seconds; much longer than the timescales identified in psychophysiological studies for normal preparation for voluntary action. We have used a combination of sensorimotor rhythms and motor imagery training to decode intentions in a single-trial cued-response paradigm similar to those used in human and non-human primate motor control research. Decoding accuracy of over 0.83 was achieved with twelve participants. With this approach, we could decode intentions to move the left or right hand at sub-second timescales, both for instructed choices instructed by an external stimulus and for free choices generated intentionally by the participant. The implications for volition are considered.

  18. Decoding the TV Remote Control.

    Science.gov (United States)

    O'Connell, James

    2000-01-01

    Describes how to observe the pulse structure of the infrared signals from the light-emitting diode in a TV remote control. This exercise in decoding infrared digital signals provides an opportunity to discuss semiconductors, photonics technology, cryptology, and the physics of how things work. (WRM)

  19. Improved decoding for a concatenated coding system

    DEFF Research Database (Denmark)

    Paaske, Erik

    1990-01-01

    The concatenated coding system recommended by CCSDS (Consultative Committee for Space Data Systems) uses an outer (255,233) Reed-Solomon (RS) code based on 8-b symbols, followed by the block interleaver and an inner rate 1/2 convolutional code with memory 6. Viterbi decoding is assumed. Two new...... decoding procedures based on repeated decoding trials and exchange of information between the two decoders and the deinterleaver are proposed. In the first one, where the improvement is 0.3-0.4 dB, only the RS decoder performs repeated trials. In the second one, where the improvement is 0.5-0.6 dB, both...

  20. On Decoding Interleaved Chinese Remainder Codes

    DEFF Research Database (Denmark)

    Li, Wenhui; Sidorenko, Vladimir; Nielsen, Johan Sebastian Rosenkilde

    2013-01-01

    We model the decoding of Interleaved Chinese Remainder codes as that of finding a short vector in a Z-lattice. Using the LLL algorithm, we obtain an efficient decoding algorithm, correcting errors beyond the unique decoding bound and having nearly linear complexity. The algorithm can fail...... with a probability dependent on the number of errors, and we give an upper bound for this. Simulation results indicate that the bound is close to the truth. We apply the proposed decoding algorithm for decoding a single CR code using the idea of “Power” decoding, suggested for Reed-Solomon codes. A combination...... of these two methods can be used to decode low-rate Interleaved Chinese Remainder codes....

  1. Iterative Demodulation and Decoding Scheme with 16QAM

    Institute of Scientific and Technical Information of China (English)

    LIU Lin-nan; KUANG Jing-ming; LI Ming; FEI Ze-song

    2006-01-01

    Iterative demodulation and decoding scheme is analyzed and modulation labeling is considered to be one of the crucial factors to this scheme. By analyzing the existent mapping design criterion, four aspects are found as the key techniques for choosing a label mapping. Based on this discovery, a novel mapping design criterion is proposed and two label mappings are searched according to it. Simulation results show that the performance of BICM-ID using the novel mappings is better than the former ones. The extrinsic information transfer(EXIT) chart is introduced and it is used to evaluate the proposed mapping design criteria.

  2. Multichannel Error Correction Code Decoder

    Science.gov (United States)

    1996-01-01

    NASA Lewis Research Center's Digital Systems Technology Branch has an ongoing program in modulation, coding, onboard processing, and switching. Recently, NASA completed a project to incorporate a time-shared decoder into the very-small-aperture terminal (VSAT) onboard-processing mesh architecture. The primary goal was to demonstrate a time-shared decoder for a regenerative satellite that uses asynchronous, frequency-division multiple access (FDMA) uplink channels, thereby identifying hardware and power requirements and fault-tolerant issues that would have to be addressed in a operational system. A secondary goal was to integrate and test, in a system environment, two NASA-sponsored, proof-of-concept hardware deliverables: the Harris Corp. high-speed Bose Chaudhuri-Hocquenghem (BCH) codec and the TRW multichannel demultiplexer/demodulator (MCDD). A beneficial byproduct of this project was the development of flexible, multichannel-uplink signal-generation equipment.

  3. Fingerprinting with Minimum Distance Decoding

    CERN Document Server

    Lin, Shih-Chun; Gamal, Hesham El

    2007-01-01

    This work adopts an information theoretic framework for the design of collusion-resistant coding/decoding schemes for digital fingerprinting. More specifically, the minimum distance decision rule is used to identify 1 out of t pirates. Achievable rates, under this detection rule, are characterized in two distinct scenarios. First, we consider the averaging attack where a random coding argument is used to show that the rate 1/2 is achievable with t=2 pirates. Our study is then extended to the general case of arbitrary $t$ highlighting the underlying complexity-performance tradeoff. Overall, these results establish the significant performance gains offered by minimum distance decoding as compared to other approaches based on orthogonal codes and correlation detectors. In the second scenario, we characterize the achievable rates, with minimum distance decoding, under any collusion attack that satisfies the marking assumption. For t=2 pirates, we show that the rate $1-H(0.25)\\approx 0.188$ is achievable using an ...

  4. LDPC Decoding on GPU for Mobile Device

    Directory of Open Access Journals (Sweden)

    Yiqin Lu

    2016-01-01

    Full Text Available A flexible software LDPC decoder that exploits data parallelism for simultaneous multicode words decoding on the mobile device is proposed in this paper, supported by multithreading on OpenCL based graphics processing units. By dividing the check matrix into several parts to make full use of both the local memory and private memory on GPU and properly modify the code capacity each time, our implementation on a mobile phone shows throughputs above 100 Mbps and delay is less than 1.6 millisecond in decoding, which make high-speed communication like video calling possible. To realize efficient software LDPC decoding on the mobile device, the LDPC decoding feature on communication baseband chip should be replaced to save the cost and make it easier to upgrade decoder to be compatible with a variety of channel access schemes.

  5. Towards joint decoding of Tardos fingerprinting codes

    CERN Document Server

    Meerwald, Peter

    2011-01-01

    The class of joint decoder of probabilistic fingerprinting codes is of utmost importance in theoretical papers to establish the concept of fingerprint capacity. However, no implementation supporting a large user base is known to date. This paper presents an iterative decoder which is, as far as we are aware of, the first practical attempt towards joint decoding. The discriminative feature of the scores benefits on one hand from the side-information of previously accused users, and on the other hand, from recently introduced universal linear decoders for compound channels. Neither the code construction nor the decoder make precise assumptions about the collusion (size or strategy). The extension to incorporate soft outputs from the watermarking layer is straightforward. An intensive experimental work benchmarks the very good performances and offers a clear comparison with previous state-of-the-art decoders.

  6. Reduced-Latency SC Polar Decoder Architectures

    CERN Document Server

    Zhang, Chuan; Parhi, Keshab K

    2011-01-01

    Polar codes have become one of the most favorable capacity achieving error correction codes (ECC) along with their simple encoding method. However, among the very few prior successive cancellation (SC) polar decoder designs, the required long code length makes the decoding latency high. In this paper, conventional decoding algorithm is transformed with look-ahead techniques. This reduces the decoding latency by 50%. With pipelining and parallel processing schemes, a parallel SC polar decoder is proposed. Sub-structure sharing approach is employed to design the merged processing element (PE). Moreover, inspired by the real FFT architecture, this paper presents a novel input generating circuit (ICG) block that can generate additional input signals for merged PEs on-the-fly. Gate-level analysis has demonstrated that the proposed design shows advantages of 50% decoding latency and twice throughput over the conventional one with similar hardware cost.

  7. Just-in-time adaptive decoder engine: a universal video decoder based on MPEG RVC

    OpenAIRE

    Gorin, Jérôme; Yviquel, Hervé; Prêteux, Françoise; Raulet, Mickaël

    2011-01-01

    International audience; In this paper, we introduce the Just-In-Time Adaptive Decoder Engine (Jade) project, which is shipped as part of the Open RVC-CAL Compiler (Orcc) project. Orcc provides a set of open-source software tools for managing decoders standardized within MPEG by the Reconfigurable Video Coding (RVC) experts. In this framework, Jade acts as a Virtual Machine for any decoder description that uses the MPEG RVC paradigm. Jade dynamically generates a native decoder representation s...

  8. A class of Sudan-decodable codes

    DEFF Research Database (Denmark)

    Nielsen, Rasmus Refslund

    2000-01-01

    In this article, Sudan's algorithm is modified into an efficient method to list-decode a class of codes which can be seen as a generalization of Reed-Solomon codes. The algorithm is specialized into a very efficient method for unique decoding. The code construction can be generalized based...... on algebraic-geometry codes and the decoding algorithms are generalized accordingly. Comparisons with Reed-Solomon and Hermitian codes are made....

  9. Toric Codes, Multiplicative Structure and Decoding

    DEFF Research Database (Denmark)

    Hansen, Johan Peder

    2017-01-01

    Long linear codes constructed from toric varieties over finite fields, their multiplicative structure and decoding. The main theme is the inherent multiplicative structure on toric codes. The multiplicative structure allows for \\emph{decoding}, resembling the decoding of Reed-Solomon codes...... and aligns with decoding by error correcting pairs. We have used the multiplicative structure on toric codes to construct linear secret sharing schemes with \\emph{strong multiplication} via Massey's construction generalizing the Shamir Linear secret sharing shemes constructed from Reed-Solomon codes. We have...... constructed quantum error correcting codes from toric surfaces by the Calderbank-Shor-Steane method....

  10. Analysis of peeling decoder for MET ensembles

    CERN Document Server

    Hinton, Ryan

    2009-01-01

    The peeling decoder introduced by Luby, et al. allows analysis of LDPC decoding for the binary erasure channel (BEC). For irregular ensembles, they analyze the decoder state as a Markov process and present a solution to the differential equations describing the process mean. Multi-edge type (MET) ensembles allow greater precision through specifying graph connectivity. We generalize the the peeling decoder for MET ensembles and derive analogous differential equations. We offer a new change of variables and solution to the node fraction evolutions in the general (MET) case. This result is preparatory to investigating finite-length ensemble behavior.

  11. Improved decoding for a concatenated coding system

    OpenAIRE

    Paaske, Erik

    1990-01-01

    The concatenated coding system recommended by CCSDS (Consultative Committee for Space Data Systems) uses an outer (255,233) Reed-Solomon (RS) code based on 8-b symbols, followed by the block interleaver and an inner rate 1/2 convolutional code with memory 6. Viterbi decoding is assumed. Two new decoding procedures based on repeated decoding trials and exchange of information between the two decoders and the deinterleaver are proposed. In the first one, where the improvement is 0.3-0.4 dB, onl...

  12. Application of Beyond Bound Decoding for High Speed Optical Communications

    DEFF Research Database (Denmark)

    Li, Bomin; Larsen, Knud J.; Vegas Olmos, Juan José;

    2013-01-01

    This paper studies the application of beyond bound decoding method for high speed optical communications. This hard-decision decoding method outperforms traditional minimum distance decoding method, with a total net coding gain of 10.36 dB.......This paper studies the application of beyond bound decoding method for high speed optical communications. This hard-decision decoding method outperforms traditional minimum distance decoding method, with a total net coding gain of 10.36 dB....

  13. Concatenated coding system with iterated sequential inner decoding

    DEFF Research Database (Denmark)

    Jensen, Ole Riis; Paaske, Erik

    1995-01-01

    We describe a concatenated coding system with iterated sequential inner decoding. The system uses convolutional codes of very long constraint length and operates on iterations between an inner Fano decoder and an outer Reed-Solomon decoder......We describe a concatenated coding system with iterated sequential inner decoding. The system uses convolutional codes of very long constraint length and operates on iterations between an inner Fano decoder and an outer Reed-Solomon decoder...

  14. HeliCis: a DNA motif discovery tool for colocalized motif pairs with periodic spacing

    Directory of Open Access Journals (Sweden)

    Mostad Petter

    2007-10-01

    Full Text Available Abstract Background Correct temporal and spatial gene expression during metazoan development relies on combinatorial interactions between different transcription factors. As a consequence, cis-regulatory elements often colocalize in clusters termed cis-regulatory modules. These may have requirements on organizational features such as spacing, order and helical phasing (periodic spacing between binding sites. Due to the turning of the DNA helix, a small modification of the distance between a pair of sites may sometimes drastically disrupt function, while insertion of a full helical turn of DNA (10–11 bp between cis elements may cause functionality to be restored. Recently, de novo motif discovery methods which incorporate organizational properties such as colocalization and order preferences have been developed, but there are no tools which incorporate periodic spacing into the model. Results We have developed a web based motif discovery tool, HeliCis, which features a flexible model which allows de novo detection of motifs with periodic spacing. Depending on the parameter settings it may also be used for discovering colocalized motifs without periodicity or motifs separated by a fixed gap of known or unknown length. We show on simulated data that it can efficiently capture the synergistic effects of colocalization and periodic spacing to improve detection of weak DNA motifs. It provides a simple to use web interface which interactively visualizes the current settings and thereby makes it easy to understand the parameters and the model structure. Conclusion HeliCis provides simple and efficient de novo discovery of colocalized DNA motif pairs, with or without periodic spacing. Our evaluations show that it can detect weak periodic patterns which are not easily discovered using a sequential approach, i.e. first finding the binding sites and second analyzing the properties of their pairwise distances.

  15. Polytope of Correct (Linear Programming) Decoding and Low-Weight Pseudo-Codewords

    CERN Document Server

    Chertkov, Michael

    2011-01-01

    We analyze Linear Programming (LP) decoding of graphical binary codes operating over soft-output, symmetric and log-concave channels. We show that the error-surface, separating domain of the correct decoding from domain of the erroneous decoding, is a polytope. We formulate the problem of finding the lowest-weight pseudo-codeword as a non-convex optimization (maximization of a convex function) over a polytope, with the cost function defined by the channel and the polytope defined by the structure of the code. This formulation suggests new heuristics for finding the lowest weight pseudo-codewords, which is advantageous in comparison with the one discussed previously, in particular because of being provably monotonic and also resulting in more frequent discoveries of pseudo-codewords with the lowest weights. The algorithm performance is tested on the example of the Tanner [155, 64, 20] code over the Additive White Gaussian Noise (AWGN) channel.

  16. Decoding Generalized Reed-Solomon Codes and Its Application to RLCE Encryption Schemes

    OpenAIRE

    Wang, Yongge

    2017-01-01

    This paper presents a survey on generalized Reed-Solomon codes and various decoding algorithms: Berlekamp-Massey decoding algorithms; Berlekamp-Welch decoding algorithms; Euclidean decoding algorithms; discrete Fourier decoding algorithms, Chien's search algorithm, and Forney's algorithm.

  17. On minimizing the maximum broadcast decoding delay for instantly decodable network coding

    KAUST Repository

    Douik, Ahmed S.

    2014-09-01

    In this paper, we consider the problem of minimizing the maximum broadcast decoding delay experienced by all the receivers of generalized instantly decodable network coding (IDNC). Unlike the sum decoding delay, the maximum decoding delay as a definition of delay for IDNC allows a more equitable distribution of the delays between the different receivers and thus a better Quality of Service (QoS). In order to solve this problem, we first derive the expressions for the probability distributions of maximum decoding delay increments. Given these expressions, we formulate the problem as a maximum weight clique problem in the IDNC graph. Although this problem is known to be NP-hard, we design a greedy algorithm to perform effective packet selection. Through extensive simulations, we compare the sum decoding delay and the max decoding delay experienced when applying the policies to minimize the sum decoding delay and our policy to reduce the max decoding delay. Simulations results show that our policy gives a good agreement among all the delay aspects in all situations and outperforms the sum decoding delay policy to effectively minimize the sum decoding delay when the channel conditions become harsher. They also show that our definition of delay significantly improve the number of served receivers when they are subject to strict delay constraints.

  18. Decoder for Nonbinary CWS Quantum Codes

    CERN Document Server

    Melo, Nolmar; Portugal, Renato

    2012-01-01

    We present a decoder for nonbinary CWS quantum codes using the structure of union codes. The decoder runs in two steps: first we use a union of stabilizer codes to detect a sequence of errors, and second we build a new code, called union code, that allows to correct the errors.

  19. Overview of Decoding across the Disciplines

    Science.gov (United States)

    Boman, Jennifer; Currie, Genevieve; MacDonald, Ron; Miller-Young, Janice; Yeo, Michelle; Zettel, Stephanie

    2017-01-01

    In this chapter we describe the Decoding the Disciplines Faculty Learning Community at Mount Royal University and how Decoding has been used in new and multidisciplinary ways in the various teaching, curriculum, and research projects that are presented in detail in subsequent chapters.

  20. Design Space of Flexible Multigigabit LDPC Decoders

    Directory of Open Access Journals (Sweden)

    Philipp Schläfer

    2012-01-01

    Full Text Available Multigigabit LDPC decoders are demanded by standards like IEEE 802.15.3c and IEEE 802.11ad. To achieve the high throughput while supporting the needed flexibility, sophisticated architectures are mandatory. This paper comprehensively presents the design space for flexible multigigabit LDPC applications for the first time. The influence of various design parameters on the hardware is investigated in depth. Two new decoder architectures in a 65 nm CMOS technology are presented to further explore the design space. In the past, the memory domination was the bottleneck for throughputs of up to 1 Gbit/s. Our systematic investigation of column- versus row-based partially parallel decoders shows that this is no more a bottleneck for multigigabit architectures. The evolutionary progress in flexible multigigabit LDPC decoder design is highlighted in an extensive comparison of state-of-the-art decoders.

  1. rVISTA for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites

    Energy Technology Data Exchange (ETDEWEB)

    Loots, Gabriela G.; Ovcharenko, Ivan; Pachter, Lior; Dubchak, Inna; Rubin, Edward M.

    2002-03-08

    Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVISTA, for high-throughput discovery of cis-regulatory elements that combines transcription factor binding site prediction and the analysis of inter-species sequence conservation. Here, we illustrate the ability of rVISTA to identify true transcription factor binding sites through the analysis of AP-1 and NFAT binding sites in the 1 Mb well-annotated cytokine gene cluster1 (Hs5q31; Mm11). The exploitation of orthologous human-mouse data set resulted in the elimination of 95 percent of the 38,000 binding sites predicted upon analysis of the human sequence alone, while it identified 87 percent of the experimentally verified binding sites in this region.

  2. Turbo decoding using two soft output values

    Institute of Scientific and Technical Information of China (English)

    李建平; 潘申富; 梁庆林

    2004-01-01

    It is well known that turbo decoding always begins from the first component decoder and supposes that the apriori information is "0" at the first iterative decoding. To alternatively start decoding at two component decoders, we can gain two soft output values for the received observation of an input bit. It is obvious that two soft output values comprise more sufficient extrinsic information than only one output value obtained in the conventional scheme since different start points of decoding result in different combinations of the a priori information and the input codewords with different symbol orders due to the permutation of an interleaver. Summarizing two soft output values for erery bit before making hard decisions, we can correct more errors due to their complement. Consequently, turbo codes can achieve better error correcting performance than before in this way. Simulation results show that the performance of turbo codes using the novel proposed decoding scheme can get a growing improvement with the increment of SNR in general compared to the conventional scheme. When the bit error probability is 10-5, the proposed scheme can achieve 0.5 dB asymptotic coding gain or so under the given simulation conditions.

  3. Application of RS Codes in Decoding QR Code

    Institute of Scientific and Technical Information of China (English)

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

    2003-01-01

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

  4. Three phase full wave dc motor decoder

    Science.gov (United States)

    Studer, P. A. (Inventor)

    1977-01-01

    A three phase decoder for dc motors is disclosed which employs an extremely simple six transistor circuit to derive six properly phased output signals for fullwave operation of dc motors. Six decoding transistors are coupled at their base-emitter junctions across a resistor network arranged in a delta configuration. Each point of the delta configuration is coupled to one of three position sensors which sense the rotational position of the motor. A second embodiment of the invention is disclosed in which photo-optical isolators are used in place of the decoding transistors.

  5. An Encoder/Decoder Scheme of OCDMA Based on Waveguide

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A new encoder/decoder scheme of OCDMA based on waveguide isproposed in this paper. The principle as well as the structure of waveguide encoder/decoder is given. It can be seen that all-optical OCDMA encoder/decoder can be realized by the proposed scheme of the waveguide encoder/decoder. It can also make the OCDMA encoder/decoder integrated easily and the access controlled easily. The system based on this scheme can work under the entirely asynchronous condition.

  6. List Decoding Tensor Products and Interleaved Codes

    CERN Document Server

    Gopalan, Parikshit; Raghavendra, Prasad

    2008-01-01

    We design the first efficient algorithms and prove new combinatorial bounds for list decoding tensor products of codes and interleaved codes. We show that for {\\em every} code, the ratio of its list decoding radius to its minimum distance stays unchanged under the tensor product operation (rather than squaring, as one might expect). This gives the first efficient list decoders and new combinatorial bounds for some natural codes including multivariate polynomials where the degree in each variable is bounded. We show that for {\\em every} code, its list decoding radius remains unchanged under $m$-wise interleaving for an integer $m$. This generalizes a recent result of Dinur et al \\cite{DGKS}, who proved such a result for interleaved Hadamard codes (equivalently, linear transformations). Using the notion of generalized Hamming weights, we give better list size bounds for {\\em both} tensoring and interleaving of binary linear codes. By analyzing the weight distribution of these codes, we reduce the task of boundi...

  7. Decoding the Disciplines as a Hermeneutic Practice

    Science.gov (United States)

    Yeo, Michelle

    2017-01-01

    This chapter argues that expert practice is an inquiry that surfaces a hermeneutic relationship between theory, practice, and the world, with implications for new lines of questioning in the Decoding interview.

  8. Facial age affects emotional expression decoding

    OpenAIRE

    2014-01-01

    Facial expressions convey important information on emotional states of our interaction partners. However, in interactions between younger and older adults, there is evidence for a reduced ability to accurately decode emotional facial expressions. Previous studies have often followed up this phenomenon by examining the effect of the observers' age. However, decoding emotional faces is also likely to be influenced by stimulus features, and age-related changes in the face such as wrinkles and fo...

  9. Facial age affects emotional expression decoding

    OpenAIRE

    2014-01-01

    Facial expressions convey important information on emotional states of our interaction partners. However, in interactions between younger and older adults, there is evidence for a reduced ability to accurately decode emotional facial expressions.Previous studies have often followed up this phenomenon by examining the effect of the observers’ age. However, decoding emotional faces is also likely to be influenced by stimulus features, and age-related changes in the face such as wrinkles and fol...

  10. Facial age affects emotional expression decoding

    Directory of Open Access Journals (Sweden)

    Mara eFölster

    2014-02-01

    Full Text Available Facial expressions convey important information on emotional states of our interaction partners. However, in interactions between younger and older adults, there is evidence for a reduced ability to accurately decode emotional facial expressions.Previous studies have often followed up this phenomenon by examining the effect of the observers’ age. However, decoding emotional faces is also likely to be influenced by stimulus features, and age-related changes in the face such as wrinkles and folds may render facial expressions of older adults harder to decode. In this paper, we review theoretical frameworks and empirical findings on age effects on decoding emotional expressions, with an emphasis on age-of-face effects. We conclude that the age of the face plays an important role for facial expression decoding. Lower expressivity, age-related changes in the face, less elaborated emotion schemas for older faces, negative attitudes toward older adults, and different visual scan patterns and neural processing of older than younger faces may lower decoding accuracy for older faces. Furthermore, age-related stereotypes and age-related changes in the face may bias the attribution of specific emotions such as sadness to older faces.

  11. Facial age affects emotional expression decoding.

    Science.gov (United States)

    Fölster, Mara; Hess, Ursula; Werheid, Katja

    2014-01-01

    Facial expressions convey important information on emotional states of our interaction partners. However, in interactions between younger and older adults, there is evidence for a reduced ability to accurately decode emotional facial expressions. Previous studies have often followed up this phenomenon by examining the effect of the observers' age. However, decoding emotional faces is also likely to be influenced by stimulus features, and age-related changes in the face such as wrinkles and folds may render facial expressions of older adults harder to decode. In this paper, we review theoretical frameworks and empirical findings on age effects on decoding emotional expressions, with an emphasis on age-of-face effects. We conclude that the age of the face plays an important role for facial expression decoding. Lower expressivity, age-related changes in the face, less elaborated emotion schemas for older faces, negative attitudes toward older adults, and different visual scan patterns and neural processing of older than younger faces may lower decoding accuracy for older faces. Furthermore, age-related stereotypes and age-related changes in the face may bias the attribution of specific emotions such as sadness to older faces.

  12. Patterns of cis regulatory variation in diverse human populations.

    Directory of Open Access Journals (Sweden)

    Barbara E Stranger

    Full Text Available The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for the transferability of complex trait variants across populations.

  13. Computational methods to dissect cis-regulatory transcriptional networks

    Indian Academy of Sciences (India)

    Vibha Rani

    2007-12-01

    The formation of diverse cell types from an invariant set of genes is governed by biochemical and molecular processes that regulate gene activity. A complete understanding of the regulatory mechanisms of gene expression is the major function of genomics. Computational genomics is a rapidly emerging area for deciphering the regulation of metazoan genes as well as interpreting the results of high-throughput screening. The integration of computer science with biology has expedited molecular modelling and processing of large-scale data inputs such as microarrays, analysis of genomes, transcriptomes and proteomes. Many bioinformaticians have developed various algorithms for predicting transcriptional regulatory mechanisms from the sequence, gene expression and interaction data. This review contains compiled information of various computational methods adopted to dissect gene expression pathways.

  14. Patterns of cis regulatory variation in diverse human populations.

    Directory of Open Access Journals (Sweden)

    Barbara E Stranger

    Full Text Available The genetic basis of gene expression variation has long been studied with the aim to understand the landscape of regulatory variants, but also more recently to assist in the interpretation and elucidation of disease signals. To date, many studies have looked in specific tissues and population-based samples, but there has been limited assessment of the degree of inter-population variability in regulatory variation. We analyzed genome-wide gene expression in lymphoblastoid cell lines from a total of 726 individuals from 8 global populations from the HapMap3 project and correlated gene expression levels with HapMap3 SNPs located in cis to the genes. We describe the influence of ancestry on gene expression levels within and between these diverse human populations and uncover a non-negligible impact on global patterns of gene expression. We further dissect the specific functional pathways differentiated between populations. We also identify 5,691 expression quantitative trait loci (eQTLs after controlling for both non-genetic factors and population admixture and observe that half of the cis-eQTLs are replicated in one or more of the populations. We highlight patterns of eQTL-sharing between populations, which are partially determined by population genetic relatedness, and discover significant sharing of eQTL effects between Asians, European-admixed, and African subpopulations. Specifically, we observe that both the effect size and the direction of effect for eQTLs are highly conserved across populations. We observe an increasing proximity of eQTLs toward the transcription start site as sharing of eQTLs among populations increases, highlighting that variants close to TSS have stronger effects and therefore are more likely to be detected across a wider panel of populations. Together these results offer a unique picture and resource of the degree of differentiation among human populations in functional regulatory variation and provide an estimate for the transferability of complex trait variants across populations.

  15. On Decoding Irregular Tanner Codes

    CERN Document Server

    Even, Guy

    2011-01-01

    We present a new combinatorial characterization for local-optimality of a codeword in irregular Tanner codes. This characterization is a generalization of [Arora, Daskalakis, Steurer; 2009] and [Vontobel; 2010]. The main novelty in this characterization is that it is based on a conical combination of subtrees in the computation trees. These subtrees may have any degree in the local-code nodes and may have any height (even greater than the girth). We prove that local-optimality in this new characterization implies Maximum-Likelihood (ML) optimality and LP-optimality. We also show that it is possible to compute efficiently a certificate for the local-optimality of a codeword given the channel output. We apply this characterization to regular Tanner codes. We prove a lower bound on the noise threshold in channels such as BSC and AWGNC. When the noise is below this lower bound, the probability that LP decoding fails diminishes doubly exponentially in the girth of the Tanner graph. We use local optimality also to ...

  16. Sphere decoding complexity exponent for decoding full rate codes over the quasi-static MIMO channel

    CERN Document Server

    Jalden, Joakim

    2011-01-01

    In the setting of quasi-static multiple-input multiple-output (MIMO) channels, we consider the high signal-to-noise ratio (SNR) asymptotic complexity required by the sphere decoding (SD) algorithm for decoding a large class of full rate linear space-time codes. With SD complexity having random fluctuations induced by the random channel, noise and codeword realizations, the introduced SD complexity exponent manages to concisely describe the computational reserves required by the SD algorithm to achieve arbitrarily close to optimal decoding performance. Bounds and exact expressions for the SD complexity exponent are obtained for the decoding of large families of codes with arbitrary performance characteristics. For the particular example of decoding the recently introduced threaded cyclic division algebra (CDA) based codes -- the only currently known explicit designs that are uniformly optimal with respect to the diversity multiplexing tradeoff (DMT) -- the SD complexity exponent is shown to take a particularly...

  17. Linear-programming Decoding of Non-binary Linear Codes

    CERN Document Server

    Flanagan, Mark F; Byrne, Eimear; Greferath, Marcus

    2007-01-01

    We develop a framework for linear-programming (LP) decoding of non-binary linear codes over rings. We prove that the resulting LP decoder has the `maximum likelihood certificate' property, and we show that the decoder output is the lowest cost pseudocodeword. Equivalence between pseudocodewords of the linear program and pseudocodewords of graph covers is proved. LP decoding performance is illustrated for the (11,6,5) ternary Golay code with ternary PSK modulation over AWGN, and in this case it is shown that the LP decoder performance is comparable to codeword-error-rate-optimum hard-decision based decoding.

  18. Guided Discoveries.

    Science.gov (United States)

    Ehrlich, Amos

    1991-01-01

    Presented are four mathematical discoveries made by students on an arithmetical function using the Fibonacci sequence. Discussed is the nature of the role of the teacher in directing the students' discovery activities. (KR)

  19. FPGA implementation of low complexity LDPC iterative decoder

    Science.gov (United States)

    Verma, Shivani; Sharma, Sanjay

    2016-07-01

    Low-density parity-check (LDPC) codes, proposed by Gallager, emerged as a class of codes which can yield very good performance on the additive white Gaussian noise channel as well as on the binary symmetric channel. LDPC codes have gained lots of importance due to their capacity achieving property and excellent performance in the noisy channel. Belief propagation (BP) algorithm and its approximations, most notably min-sum, are popular iterative decoding algorithms used for LDPC and turbo codes. The trade-off between the hardware complexity and the decoding throughput is a critical factor in the implementation of the practical decoder. This article presents introduction to LDPC codes and its various decoding algorithms followed by realisation of LDPC decoder by using simplified message passing algorithm and partially parallel decoder architecture. Simplified message passing algorithm has been proposed for trade-off between low decoding complexity and decoder performance. It greatly reduces the routing and check node complexity of the decoder. Partially parallel decoder architecture possesses high speed and reduced complexity. The improved design of the decoder possesses a maximum symbol throughput of 92.95 Mbps and a maximum of 18 decoding iterations. The article presents implementation of 9216 bits, rate-1/2, (3, 6) LDPC decoder on Xilinx XC3D3400A device from Spartan-3A DSP family.

  20. The limits of de novo DNA motif discovery.

    Directory of Open Access Journals (Sweden)

    David Simcha

    Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

  1. Volatility Discovery

    DEFF Research Database (Denmark)

    Dias, Gustavo Fruet; Scherrer, Cristina; Papailias, Fotis

    The price discovery literature investigates how homogenous securities traded on different markets incorporate information into prices. We take this literature one step further and investigate how these markets contribute to stochastic volatility (volatility discovery). We formally show...... that the realized measures from homogenous securities share a fractional stochastic trend, which is a combination of the price and volatility discovery measures. Furthermore, we show that volatility discovery is associated with the way that market participants process information arrival (market sensitivity...

  2. Completion time reduction in instantly decodable network coding through decoding delay control

    KAUST Repository

    Douik, Ahmed S.

    2014-12-01

    For several years, the completion time and the decoding delay problems in Instantly Decodable Network Coding (IDNC) were considered separately and were thought to completely act against each other. Recently, some works aimed to balance the effects of these two important IDNC metrics but none of them studied a further optimization of one by controlling the other. In this paper, we study the effect of controlling the decoding delay to reduce the completion time below its currently best known solution. We first derive the decoding-delay-dependent expressions of the users\\' and their overall completion times. Although using such expressions to find the optimal overall completion time is NP-hard, we use a heuristic that minimizes the probability of increasing the maximum of these decoding-delay-dependent completion time expressions after each transmission through a layered control of their decoding delays. Simulation results show that this new algorithm achieves both a lower mean completion time and mean decoding delay compared to the best known heuristic for completion time reduction. The gap in performance becomes significant for harsh erasure scenarios.

  3. Error Exponents of Optimum Decoding for the Interference Channel

    CERN Document Server

    Etkin, Raul; Ordentlich, Erik

    2008-01-01

    Exponential error bounds for the finite-alphabet interference channel (IFC) with two transmitter-receiver pairs, are investigated under the random coding regime. Our focus is on optimum decoding, as opposed to heuristic decoding rules that have been used in previous works, like joint typicality decoding, decoding based on interference cancellation, and decoding that considers the interference as additional noise. Indeed, the fact that the actual interfering signal is a codeword and not an i.i.d. noise process complicates the application of conventional techniques to the performance analysis of the optimum decoder. Using analytical tools rooted in statistical physics, we derive a single letter expression for error exponents achievable under optimum decoding and demonstrate strict improvement over error exponents obtainable using suboptimal decoding rules, but which are amenable to more conventional analysis.

  4. Decoding of concatenated codes with interleaved outer codes

    DEFF Research Database (Denmark)

    Justesen, Jørn; Thommesen, Christian; Høholdt, Tom

    2004-01-01

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

  5. VLSI Design of a Turbo Decoder

    Science.gov (United States)

    Fang, Wai-Chi

    2007-01-01

    A very-large-scale-integrated-circuit (VLSI) turbo decoder has been designed to serve as a compact, high-throughput, low-power, lightweight decoder core of a receiver in a data-communication system. In a typical contemplated application, such a decoder core would be part of a single integrated circuit that would include the rest of the receiver circuitry and possibly some or all of the transmitter circuitry, all designed and fabricated together according to an advanced communication-system-on-a-chip design concept. Turbo codes are forward-error-correction (FEC) codes. Relative to older FEC codes, turbo codes enable communication at lower signal-to-noise ratios and offer greater coding gain. In addition, turbo codes can be implemented by relatively simple hardware. Therefore, turbo codes have been adopted as standard for some advanced broadband communication systems.

  6. Online Testable Decoder using Reversible Logic

    Directory of Open Access Journals (Sweden)

    Hemalatha. K. N. Manjula B. B. Girija. S

    2012-02-01

    Full Text Available The project proposes to design and test 2 to 4 reversible Decoder circuit with arbitrary number of gates to an online testable reversible one and is independent of the type of reversible gate used. The constructed circuit can detect any single bit errors and to convert a decoder circuit that is designed by reversible gates to an online testable reversible decoder circuit. Conventional digital circuits dissipate a significant amount of energy because bits of information are erased during the logic operations. Thus if logic gates are designed such that the information bits are not destroyed, the power consumption can be reduced. The information bits are not lost in case of a reversible computation. Reversible logic can be used to implement any Boolean logic function.

  7. Neuroprosthetic Decoder Training as Imitation Learning.

    Directory of Open Access Journals (Sweden)

    Josh Merel

    2016-05-01

    Full Text Available Neuroprosthetic brain-computer interfaces function via an algorithm which decodes neural activity of the user into movements of an end effector, such as a cursor or robotic arm. In practice, the decoder is often learned by updating its parameters while the user performs a task. When the user's intention is not directly observable, recent methods have demonstrated value in training the decoder against a surrogate for the user's intended movement. Here we show that training a decoder in this way is a novel variant of an imitation learning problem, where an oracle or expert is employed for supervised training in lieu of direct observations, which are not available. Specifically, we describe how a generic imitation learning meta-algorithm, dataset aggregation (DAgger, can be adapted to train a generic brain-computer interface. By deriving existing learning algorithms for brain-computer interfaces in this framework, we provide a novel analysis of regret (an important metric of learning efficacy for brain-computer interfaces. This analysis allows us to characterize the space of algorithmic variants and bounds on their regret rates. Existing approaches for decoder learning have been performed in the cursor control setting, but the available design principles for these decoders are such that it has been impossible to scale them to naturalistic settings. Leveraging our findings, we then offer an algorithm that combines imitation learning with optimal control, which should allow for training of arbitrary effectors for which optimal control can generate goal-oriented control. We demonstrate this novel and general BCI algorithm with simulated neuroprosthetic control of a 26 degree-of-freedom model of an arm, a sophisticated and realistic end effector.

  8. Generalized Sudan's List Decoding for Order Domain Codes

    DEFF Research Database (Denmark)

    Geil, Hans Olav; Matsumoto, Ryutaroh

    2007-01-01

    We generalize Sudan's list decoding algorithm without multiplicity to evaluation codes coming from arbitrary order domains. The number of correctable errors by the proposed method is larger than the original list decoding without multiplicity.......We generalize Sudan's list decoding algorithm without multiplicity to evaluation codes coming from arbitrary order domains. The number of correctable errors by the proposed method is larger than the original list decoding without multiplicity....

  9. Generalized Sudan's List Decoding for Order Domain Codes

    DEFF Research Database (Denmark)

    Geil, Hans Olav; Matsumoto, Ryutaroh

    2007-01-01

    We generalize Sudan's list decoding algorithm without multiplicity to evaluation codes coming from arbitrary order domains. The number of correctable errors by the proposed method is larger than the original list decoding without multiplicity.......We generalize Sudan's list decoding algorithm without multiplicity to evaluation codes coming from arbitrary order domains. The number of correctable errors by the proposed method is larger than the original list decoding without multiplicity....

  10. LP Decoding meets LP Decoding: A Connection between Channel Coding and Compressed Sensing

    CERN Document Server

    Dimakis, Alexandros G

    2009-01-01

    This is a tale of two linear programming decoders, namely channel coding linear programming decoding (CC-LPD) and compressed sensing linear programming decoding (CS-LPD). So far, they have evolved quite independently. The aim of the present paper is to show that there is a tight connection between, on the one hand, CS-LPD based on a zero-one measurement matrix over the reals and, on the other hand, CC-LPD of the binary linear code that is obtained by viewing this measurement matrix as a binary parity-check matrix. This connection allows one to translate performance guarantees from one setup to the other.

  11. Decoding Interleaved Gabidulin Codes using Alekhnovich's Algorithm

    DEFF Research Database (Denmark)

    Puchinger, Sven; Müelich, Sven; Mödinger, David

    2017-01-01

    We prove that Alekhnovich's algorithm can be used for row reduction of skew polynomial matrices. This yields an O(ℓ3n(ω+1)/2log⁡(n)) decoding algorithm for ℓ-Interleaved Gabidulin codes of length n, where ω is the matrix multiplication exponent.......We prove that Alekhnovich's algorithm can be used for row reduction of skew polynomial matrices. This yields an O(ℓ3n(ω+1)/2log⁡(n)) decoding algorithm for ℓ-Interleaved Gabidulin codes of length n, where ω is the matrix multiplication exponent....

  12. Bounds on List Decoding Gabidulin Codes

    CERN Document Server

    Wachter-Zeh, Antonia

    2012-01-01

    An open question about Gabidulin codes is whether polynomial-time list decoding beyond half the minimum distance is possible or not. In this contribution, we give a lower and an upper bound on the list size, i.e., the number of codewords in a ball around the received word. The lower bound shows that if the radius of this ball is greater than the Johnson radius, this list size can be exponential and hence, no polynomial-time list decoding is possible. The upper bound on the list size uses subspace properties.

  13. MAP decoding of variable length codes over noisy channels

    Science.gov (United States)

    Yao, Lei; Cao, Lei; Chen, Chang Wen

    2005-10-01

    In this paper, we discuss the maximum a-posteriori probability (MAP) decoding of variable length codes(VLCs) and propose a novel decoding scheme for the Huffman VLC coded data in the presence of noise. First, we provide some simulation results of VLC MAP decoding and highlight some features that have not been discussed yet in existing work. We will show that the improvement of MAP decoding over the conventional VLC decoding comes mostly from the memory information in the source and give some observations regarding the advantage of soft VLC MAP decoding over hard VLC MAP decoding when AWGN channel is considered. Second, with the recognition that the difficulty in VLC MAP decoding is the lack of synchronization between the symbol sequence and the coded bit sequence, which makes the parsing from the latter to the former extremely complex, we propose a new MAP decoding algorithm by integrating the information of self-synchronization strings (SSSs), one important feature of the codeword structure, into the conventional MAP decoding. A consistent performance improvement and decoding complexity reduction over the conventional VLC MAP decoding can be achieved with the new scheme.

  14. TC81201F MPEG2 decoder LSI; MPEG2 decoder LSI TC81201F

    Energy Technology Data Exchange (ETDEWEB)

    Kitagaki, K. [Toshiba Corp., Tokyo (Japan)

    1996-04-01

    The moving picture expert group 2 (MPEG2) decoder LSI series have been developed, in order to meet needs for diversifying multi-media systems. MPEG2 is an international standard for coding moving pictures, capable of compressing large quantities of moving picture data. Therefore, the decoder LSI for the MPEG2 signals is also a key device to realize the multi-media systems. The system needs are diversifying, as seen in different audio codes for DVD`s and digital satellite broadcasting systems (DBS`s). The company has developed, based on decoder LSI T9556 announced in 1994, TC81200F for mass production, TC81201F optimized for the DVD system and TC81211F as the one-chip device for MPEG1 decoder. Chip cost and system cost of TC81201F are reduced by optimizing functions and circuits, and by reducing external memories. 4 refs., 4 figs., 1 tab.

  15. Decoding Algorithms for Random Linear Network Codes

    DEFF Research Database (Denmark)

    Heide, Janus; Pedersen, Morten Videbæk; Fitzek, Frank

    2011-01-01

    achieve a high coding throughput, and reduce energy consumption.We use an on-the-fly version of the Gauss-Jordan algorithm as a baseline, and provide several simple improvements to reduce the number of operations needed to perform decoding. Our tests show that the improvements can reduce the number...

  16. Older Adults Have Difficulty in Decoding Sarcasm

    Science.gov (United States)

    Phillips, Louise H.; Allen, Roy; Bull, Rebecca; Hering, Alexandra; Kliegel, Matthias; Channon, Shelley

    2015-01-01

    Younger and older adults differ in performance on a range of social-cognitive skills, with older adults having difficulties in decoding nonverbal cues to emotion and intentions. Such skills are likely to be important when deciding whether someone is being sarcastic. In the current study we investigated in a life span sample whether there are…

  17. A chemical system that mimics decoding operations.

    Science.gov (United States)

    Giansante, Carlo; Ceroni, Paola; Venturi, Margherita; Sakamoto, Junji; Schlüter, A Dieter

    2009-02-23

    The chemical information stored in equilibrium mixtures of molecular species is larger than the sum of information carried by the individual molecules. Protonation equilibria in dilute dichloromethane solution of a shape-persistent macrocycle bearing two 2,2'-bipyridine units and two Coumarin 2 moieties (see figure) can be exploited to mimic decoding operations.

  18. Sudan-decoding generalized geometric Goppa codes

    DEFF Research Database (Denmark)

    Heydtmann, Agnes Eileen

    2003-01-01

    Generalized geometric Goppa codes are vector spaces of n-tuples with entries from different extension fields of a ground field. They are derived from evaluating functions similar to conventional geometric Goppa codes, but allowing evaluation in places of arbitrary degree. A decoding scheme...

  19. BCS-18A command decoder-selector

    Science.gov (United States)

    Laping, H.

    1980-08-01

    This report describes an 18-channel command decoder-selector which operates in conjunction with an HF command receiver to allow secure and reliable radio control of high altitude balloon payloads. A detailed technical description and test results are also included.

  20. Deconstructing multivariate decoding for the study of brain function.

    Science.gov (United States)

    Hebart, Martin N; Baker, Chris I

    2017-08-04

    Multivariate decoding methods were developed originally as tools to enable accurate predictions in real-world applications. The realization that these methods can also be employed to study brain function has led to their widespread adoption in the neurosciences. However, prior to the rise of multivariate decoding, the study of brain function was firmly embedded in a statistical philosophy grounded on univariate methods of data analysis. In this way, multivariate decoding for brain interpretation grew out of two established frameworks: multivariate decoding for predictions in real-world applications, and classical univariate analysis based on the study and interpretation of brain activation. We argue that this led to two confusions, one reflecting a mixture of multivariate decoding for prediction or interpretation, and the other a mixture of the conceptual and statistical philosophies underlying multivariate decoding and classical univariate analysis. Here we attempt to systematically disambiguate multivariate decoding for the study of brain function from the frameworks it grew out of. After elaborating these confusions and their consequences, we describe six, often unappreciated, differences between classical univariate analysis and multivariate decoding. We then focus on how the common interpretation of what is signal and noise changes in multivariate decoding. Finally, we use four examples to illustrate where these confusions may impact the interpretation of neuroimaging data. We conclude with a discussion of potential strategies to help resolve these confusions in interpreting multivariate decoding results, including the potential departure from multivariate decoding methods for the study of brain function. Copyright © 2017. Published by Elsevier Inc.

  1. Unsupervised adaptation of brain machine interface decoders

    Directory of Open Access Journals (Sweden)

    Tayfun eGürel

    2012-11-01

    Full Text Available The performance of neural decoders can degrade over time due to nonstationarities in the relationship between neuronal activity and behavior. In this case, brain-machine interfaces (BMI require adaptation of their decoders to maintain high performance across time. One way to achieve this is by use of periodical calibration phases, during which the BMI system (or an external human demonstrator instructs the user to perform certain movements or behaviors. This approach has two disadvantages: (i calibration phases interrupt the autonomous operation of the BMI and (ii between two calibration phases the BMI performance might not be stable but continuously decrease. A better alternative would be that the BMI decoder is able to continuously adapt in an unsupervised manner during autonomous BMI operation, i.e. without knowing the movement intentions of the user. In the present article, we present an efficient method for such unsupervised training of BMI systems for continuous movement control. The proposed method utilizes a cost function derived from neuronal recordings, which guides a learning algorithm to evaluate the decoding parameters. We verify the performance of our adaptive method by simulating a BMI user with an optimal feedback control model and its interaction with our adaptive BMI decoder. The simulation results show that the cost function and the algorithm yield fast and precise trajectories towards targets at random orientations on a 2-dimensional computer screen. For initially unknown and nonstationary tuning parameters, our unsupervised method is still able to generate precise trajectories and to keep its performance stable in the long term. The algorithm can optionally work also with neuronal error signals instead or in conjunction with the proposed unsupervised adaptation.

  2. Belief propagation decoding of quantum channels by passing quantum messages

    Science.gov (United States)

    Renes, Joseph M.

    2017-07-01

    The belief propagation (BP) algorithm is a powerful tool in a wide range of disciplines from statistical physics to machine learning to computational biology, and is ubiquitous in decoding classical error-correcting codes. The algorithm works by passing messages between nodes of the factor graph associated with the code and enables efficient decoding of the channel, in some cases even up to the Shannon capacity. Here we construct the first BP algorithm which passes quantum messages on the factor graph and is capable of decoding the classical-quantum channel with pure state outputs. This gives explicit decoding circuits whose number of gates is quadratic in the code length. We also show that this decoder can be modified to work with polar codes for the pure state channel and as part of a decoder for transmitting quantum information over the amplitude damping channel. These represent the first explicit capacity-achieving decoders for non-Pauli channels.

  3. Efficient Decoding of Turbo Codes with Nonbinary Belief Propagation

    Directory of Open Access Journals (Sweden)

    Thierry Lestable

    2008-05-01

    Full Text Available This paper presents a new approach to decode turbo codes using a nonbinary belief propagation decoder. The proposed approach can be decomposed into two main steps. First, a nonbinary Tanner graph representation of the turbo code is derived by clustering the binary parity-check matrix of the turbo code. Then, a group belief propagation decoder runs several iterations on the obtained nonbinary Tanner graph. We show in particular that it is necessary to add a preprocessing step on the parity-check matrix of the turbo code in order to ensure good topological properties of the Tanner graph and then good iterative decoding performance. Finally, by capitalizing on the diversity which comes from the existence of distinct efficient preprocessings, we propose a new decoding strategy, called decoder diversity, that intends to take benefits from the diversity through collaborative decoding schemes.

  4. Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes. Part 3; The Map and Related Decoding Algirithms

    Science.gov (United States)

    Lin, Shu; Fossorier, Marc

    1998-01-01

    In a coded communication system with equiprobable signaling, MLD minimizes the word error probability and delivers the most likely codeword associated with the corresponding received sequence. This decoding has two drawbacks. First, minimization of the word error probability is not equivalent to minimization of the bit error probability. Therefore, MLD becomes suboptimum with respect to the bit error probability. Second, MLD delivers a hard-decision estimate of the received sequence, so that information is lost between the input and output of the ML decoder. This information is important in coded schemes where the decoded sequence is further processed, such as concatenated coding schemes, multi-stage and iterative decoding schemes. In this chapter, we first present a decoding algorithm which both minimizes bit error probability, and provides the corresponding soft information at the output of the decoder. This algorithm is referred to as the MAP (maximum aposteriori probability) decoding algorithm.

  5. On Lattice Sequential Decoding for The Unconstrained AWGN Channel

    KAUST Repository

    Abediseid, Walid

    2013-04-04

    In this paper, the performance limits and the computational complexity of the lattice sequential decoder are analyzed for the unconstrained additive white Gaussian noise channel. The performance analysis available in the literature for such a channel has been studied only under the use of the minimum Euclidean distance decoder that is commonly referred to as the \\\\textit{lattice decoder}. Lattice decoders based on solutions to the NP-hard closest vector problem are very complex to implement, and the search for low complexity receivers for the detection of lattice codes is considered a challenging problem. However, the low computational complexity advantage that sequential decoding promises, makes it an alternative solution to the lattice decoder. In this work, we characterize the performance and complexity tradeoff via the error exponent and the decoding complexity, respectively, of such a decoder as a function of the decoding parameter --- the bias term. For the above channel, we derive the cut-off volume-to-noise ratio that is required to achieve a good error performance with low decoding complexity.

  6. On Lattice Sequential Decoding for The Unconstrained AWGN Channel

    KAUST Repository

    Abediseid, Walid

    2012-10-01

    In this paper, the performance limits and the computational complexity of the lattice sequential decoder are analyzed for the unconstrained additive white Gaussian noise channel. The performance analysis available in the literature for such a channel has been studied only under the use of the minimum Euclidean distance decoder that is commonly referred to as the lattice decoder. Lattice decoders based on solutions to the NP-hard closest vector problem are very complex to implement, and the search for low complexity receivers for the detection of lattice codes is considered a challenging problem. However, the low computational complexity advantage that sequential decoding promises, makes it an alternative solution to the lattice decoder. In this work, we characterize the performance and complexity tradeoff via the error exponent and the decoding complexity, respectively, of such a decoder as a function of the decoding parameter --- the bias term. For the above channel, we derive the cut-off volume-to-noise ratio that is required to achieve a good error performance with low decoding complexity.

  7. Space vehicle Viterbi decoder. [data converters, algorithms

    Science.gov (United States)

    1975-01-01

    The design and fabrication of an extremely low-power, constraint-length 7, rate 1/3 Viterbi decoder brassboard capable of operating at information rates of up to 100 kb/s is presented. The brassboard is partitioned to facilitate a later transition to an LSI version requiring even less power. The effect of soft-decision thresholds, path memory lengths, and output selection algorithms on the bit error rate is evaluated. A branch synchronization algorithm is compared with a more conventional approach. The implementation of the decoder and its test set (including all-digital noise source) are described along with the results of various system tests and evaluations. Results and recommendations are presented.

  8. High Speed Frame Synchronization and Viterbi Decoding

    DEFF Research Database (Denmark)

    Paaske, Erik; Justesen, Jørn; Larsen, Knud J.

    1998-01-01

    The study has been divided into two phases. The purpose of Phase 1 of the study was to describe the system structure and algorithms in sufficient detail to allow drawing the high level architecture of units containing frame synchronization and Viterbi decoding. After selection of which specific...... separated by a sync marker and protected by error-correcting codes. We first give a survey of trends within the area of space modulation systems. We then discuss and define the interfaces and operating modes of the relevant system components. We present a list of system configurations that we find...... potentially useful.Algorithms for frame synchronization are described and analyzed. Further, the high level architecture of units that contain frame synchronization and various other functions needed in a complete system is presented. Two such units are described, one for placement before the Viterbi decoder...

  9. High Speed Frame Synchronization and Viterbi Decoding

    DEFF Research Database (Denmark)

    Paaske, Erik; Justesen, Jørn; Larsen, Knud J.

    1996-01-01

    The purpose of Phase 1 of the study is to describe the system structure and algorithms in sufficient detail to allow drawing the high level architecture of units containing frame synchronization and Viterbi decoding. The systems we consider are high data rate space communication systems. Also......, the systems use some form of QPSK modulation and transmit data in frames separated by a sync marker and protected by error-correcting codes. We first give a survey of trends within the area of space modulation systems. We then discuss and define the interfaces and operating modes of the relevant system...... components. Node synchronization performed within a Viterbi decoder is discussed, and algorithms for frame synchronization are described and analyzed. We present a list of system configurations that we find potentially useful. Further, the high level architecture of units that contain frame synchronization...

  10. Hardware Implementation of Serially Concatenated PPM Decoder

    Science.gov (United States)

    Moision, Bruce; Hamkins, Jon; Barsoum, Maged; Cheng, Michael; Nakashima, Michael

    2009-01-01

    A prototype decoder for a serially concatenated pulse position modulation (SCPPM) code has been implemented in a field-programmable gate array (FPGA). At the time of this reporting, this is the first known hardware SCPPM decoder. The SCPPM coding scheme, conceived for free-space optical communications with both deep-space and terrestrial applications in mind, is an improvement of several dB over the conventional Reed-Solomon PPM scheme. The design of the FPGA SCPPM decoder is based on a turbo decoding algorithm that requires relatively low computational complexity while delivering error-rate performance within approximately 1 dB of channel capacity. The SCPPM encoder consists of an outer convolutional encoder, an interleaver, an accumulator, and an inner modulation encoder (more precisely, a mapping of bits to PPM symbols). Each code is describable by a trellis (a finite directed graph). The SCPPM decoder consists of an inner soft-in-soft-out (SISO) module, a de-interleaver, an outer SISO module, and an interleaver connected in a loop (see figure). Each SISO module applies the Bahl-Cocke-Jelinek-Raviv (BCJR) algorithm to compute a-posteriori bit log-likelihood ratios (LLRs) from apriori LLRs by traversing the code trellis in forward and backward directions. The SISO modules iteratively refine the LLRs by passing the estimates between one another much like the working of a turbine engine. Extrinsic information (the difference between the a-posteriori and a-priori LLRs) is exchanged rather than the a-posteriori LLRs to minimize undesired feedback. All computations are performed in the logarithmic domain, wherein multiplications are translated into additions, thereby reducing complexity and sensitivity to fixed-point implementation roundoff errors. To lower the required memory for storing channel likelihood data and the amounts of data transfer between the decoder and the receiver, one can discard the majority of channel likelihoods, using only the remainder in

  11. Olfactory Decoding Method Using Neural Spike Signals

    Institute of Scientific and Technical Information of China (English)

    Kyung-jin YOU; Hyun-chool SHIN

    2010-01-01

    This paper presents a travel method for inferring the odor based on naval activities observed from rats'main olfactory bulbs.Mufti-channel extmcellular single unit recordings are done by microwire electrodes(Tungsten,50μm,32 channels)innplanted in the mitral/tufted cell layers of the main olfactory bulb of the anesthetized rats to obtain neural responses to various odors.Neural responses as a key feature are measured by subtraction firing rates before stimulus from after.For odor irderenoe,a decoding method is developed based on the ML estimation.The results show that the average decoding acauacy is about 100.0%,96.0%,and 80.0% with three rats,respectively.This wait has profound implications for a novel brain-madune interface system far odor inference.

  12. Decoding Split and Pool Combinatorial Libraries with Electron-Transfer Dissociation Tandem Mass Spectrometry

    Science.gov (United States)

    Sarkar, Mohosin; Pascal, Bruce D.; Steckler, Caitlin; Aquino, Claudio; Micalizio, Glenn C.; Kodadek, Thomas; Chalmers, Michael J.

    2013-07-01

    Screening of bead-based split and pool combinatorial chemistry libraries is a powerful approach to aid the discovery of new chemical compounds able to interact with, and modulate the activities of, protein targets of interest. Split and pool synthesis provides for large and well diversified chemical libraries, in this case comprised of oligomers generated from a well-defined starting set. At the end of the synthesis, each bead in the library displays many copies of a unique oligomer sequence. Because the sequence of the oligomer is not known at the time of screening, methods for decoding of the sequence of each screening "hit" are essential. Here we describe an electron-transfer dissociation (ETD) based tandem mass spectrometry approach for the decoding of mass-encoded split and pool libraries. We demonstrate that the newly described "chiral oligomers of pentenoic amides (COPAs)" yield non-sequence-specific product ions upon collisional activated dissociation; however, complete sequence information can be obtained with ETD. To aid in the decoding of libraries from MS and MS/MS data, we have incorporated 79Br/81Br isotope "tags" to differentiate N- and C-terminal product ions. In addition, we have created "Hit-Find," a software program that allows users to generate libraries in silico . The user can then search all possible members of the chemical library for those that fall within a user-defined mass error.

  13. Simplified Digital Subband Coders And Decoders

    Science.gov (United States)

    Glover, Daniel R.

    1994-01-01

    Simplified digital subband coders and decoders developed for use in converting digitized samples of source signals into compressed and encoded forms that maintain integrity of source signals while enabling transmission at low data rates. Examples of coding methods used in subbands include coarse quantization in high-frequency subbands, differential coding, predictive coding, vector quantization, and entropy or statistical coding. Encoders simpler, less expensive and operate rapidly enough to process video signals.

  14. Decoding Hermitian Codes with Sudan's Algorithm

    DEFF Research Database (Denmark)

    Høholdt, Tom; Nielsen, Rasmus Refslund

    1999-01-01

    We present an efficient implementation of Sudan's algorithm for list decoding Hermitian codes beyond half the minimum distance. The main ingredients are an explicit method to calculate so-called increasing zero bases, an efficient interpolation algorithm for finding the Q-polynomial......, and a reduction of the problem of factoring the Q-polynomial to the problem of factoring a univariate polynomial over a large finite field....

  15. DSP Specific Optimized Implementation of Viterbi Decoder

    Directory of Open Access Journals (Sweden)

    Yame Asfia

    2010-04-01

    Full Text Available Due to the rapid changing and flexibility of Wireless Communication protocols, there is a desire to move from hardware to software/firmware implementation in DSPs. High data rate requirements suggest highly optimized firmware implementation in terms of execution speed and high memory requirements. This paper suggests optimization levels for the implementation of a viable Viterbi decoding algorithm (rate ½ on a commercial off-the-shelf DSP.

  16. Kernel Temporal Differences for Neural Decoding

    Directory of Open Access Journals (Sweden)

    Jihye Bae

    2015-01-01

    Full Text Available We study the feasibility and capability of the kernel temporal difference (KTD(λ algorithm for neural decoding. KTD(λ is an online, kernel-based learning algorithm, which has been introduced to estimate value functions in reinforcement learning. This algorithm combines kernel-based representations with the temporal difference approach to learning. One of our key observations is that by using strictly positive definite kernels, algorithm’s convergence can be guaranteed for policy evaluation. The algorithm’s nonlinear functional approximation capabilities are shown in both simulations of policy evaluation and neural decoding problems (policy improvement. KTD can handle high-dimensional neural states containing spatial-temporal information at a reasonable computational complexity allowing real-time applications. When the algorithm seeks a proper mapping between a monkey’s neural states and desired positions of a computer cursor or a robot arm, in both open-loop and closed-loop experiments, it can effectively learn the neural state to action mapping. Finally, a visualization of the coadaptation process between the decoder and the subject shows the algorithm’s capabilities in reinforcement learning brain machine interfaces.

  17. Sequential decoders for large MIMO systems

    KAUST Repository

    Ali, Konpal S.

    2014-05-01

    Due to their ability to provide high data rates, multiple-input multiple-output (MIMO) systems have become increasingly popular. Decoding of these systems with acceptable error performance is computationally very demanding. In this paper, we employ the Sequential Decoder using the Fano Algorithm for large MIMO systems. A parameter called the bias is varied to attain different performance-complexity trade-offs. Low values of the bias result in excellent performance but at the expense of high complexity and vice versa for higher bias values. Numerical results are done that show moderate bias values result in a decent performance-complexity trade-off. We also attempt to bound the error by bounding the bias, using the minimum distance of a lattice. The variations in complexity with SNR have an interesting trend that shows room for considerable improvement. Our work is compared against linear decoders (LDs) aided with Element-based Lattice Reduction (ELR) and Complex Lenstra-Lenstra-Lovasz (CLLL) reduction. © 2014 IFIP.

  18. Markov source model for printed music decoding

    Science.gov (United States)

    Kopec, Gary E.; Chou, Philip A.; Maltz, David A.

    1995-03-01

    This paper describes a Markov source model for a simple subset of printed music notation. The model is based on the Adobe Sonata music symbol set and a message language of our own design. Chord imaging is the most complex part of the model. Much of the complexity follows from a rule of music typography that requires the noteheads for adjacent pitches to be placed on opposite sides of the chord stem. This rule leads to a proliferation of cases for other typographic details such as dot placement. We describe the language of message strings accepted by the model and discuss some of the imaging issues associated with various aspects of the message language. We also point out some aspects of music notation that appear problematic for a finite-state representation. Development of the model was greatly facilitated by the duality between image synthesis and image decoding. Although our ultimate objective was a music image model for use in decoding, most of the development proceeded by using the evolving model for image synthesis, since it is computationally far less costly to image a message than to decode an image.

  19. Performance Analysis of Viterbi Decoder for Wireless Applications

    Directory of Open Access Journals (Sweden)

    G.Sivasankar

    2014-07-01

    Full Text Available Viterbi decoder is employed in wireless communication to decode the convolutional codes; those codes are used in every robust digital communication systems. Convolutional encoding and viterbi decoding is a powerful method for forward error correction. This paper deals with synthesis and implementation of viterbi decoder with a constraint length of three as well as seven and the code rate of ½ in FPGA (Field Programmable Gate Array. The performance of viterbi decoder is analyzed in terms of resource utilization. The design of viterbi decoder is simulated using Verilog HDL. It is synthesized and implemented using Xilinx 9.1ise and Spartan 3E Kit. It is compatible with many common standards such as 3GPP, IEEE 802.16 and LTE.

  20. Interleaved Convolutional Code and Its Viterbi Decoder Architecture

    Directory of Open Access Journals (Sweden)

    Jun Jin Kong

    2003-12-01

    Full Text Available We propose an area-efficient high-speed interleaved Viterbi decoder architecture, which is based on the state-parallel architecture with register exchange path memory structure, for interleaved convolutional code. The state-parallel architecture uses as many add-compare-select (ACS units as the number of trellis states. By replacing each delay (or storage element in state metrics memory (or path metrics memory and path memory (or survival memory with I delays, interleaved Viterbi decoder is obtained where I is the interleaving degree. The decoding speed of this decoder architecture is as fast as the operating clock speed. The latency of proposed interleaved Viterbi decoder is “decoding depth (DD × interleaving degree (I+ extra delays (A,” which increases linearly with the interleaving degree I.

  1. A Modified max-log-MAP Decoding Algorithm for Turbo Decoding

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Turbo decoding is iterative decoding, and the MAP algorithm is optimal in terms of performance in Turbo decoding. The log-MAP algorithm is the MAP executed in the logarithmic domain, so it is also optimal. Both the MAP and the log-MAP algorithm are complicated for implementation. The max-log-MAP algorithm is derived from the log-MAP with approximation, which is simply compared with the log-MAP algorithm but is suboptimal in terms of performance. A modified max-log-MAP algorithm is presented in this paper, based on the Taylor series of logarithm and exponent. Analysis and simulation results show that the modified max-log-MAP algorithm outperforms the max-log-MAP algorithm with almost the same complexity.

  2. Decoding Delay Controlled Completion Time Reduction in Instantly Decodable Network Coding

    KAUST Repository

    Douik, Ahmed

    2016-06-27

    For several years, the completion time and the decoding delay problems in Instantly Decodable Network Coding (IDNC) were considered separately and were thought to act completely against each other. Recently, some works aimed to balance the effects of these two important IDNC metrics but none of them studied a further optimization of one by controlling the other. This paper investigates the effect of controlling the decoding delay to reduce the completion time below its currently best-known solution in both perfect and imperfect feedback with persistent erasure channels. To solve the problem, the decodingdelay- dependent expressions of the users’ and overall completion times are derived in the complete feedback scenario. Although using such expressions to find the optimal overall completion time is NP-hard, the paper proposes two novel heuristics that minimizes the probability of increasing the maximum of these decoding-delay-dependent completion time expressions after each transmission through a layered control of their decoding delays. Afterward, the paper extends the study to the imperfect feedback scenario in which uncertainties at the sender affects its ability to anticipate accurately the decoding delay increase at each user. The paper formulates the problem in such environment and derives the expression of the minimum increase in the completion time. Simulation results show the performance of the proposed solutions and suggest that both heuristics achieves a lower mean completion time as compared to the best-known heuristics for the completion time reduction in perfect and imperfect feedback. The gap in performance becomes more significant as the erasure of the channel increases.

  3. Design of a VLSI Decoder for Partially Structured LDPC Codes

    Directory of Open Access Journals (Sweden)

    Fabrizio Vacca

    2008-01-01

    of their parity matrix can be partitioned into two disjoint sets, namely, the structured and the random ones. For the proposed class of codes a constructive design method is provided. To assess the value of this method the constructed codes performance are presented. From these results, a novel decoding method called split decoding is introduced. Finally, to prove the effectiveness of the proposed approach a whole VLSI decoder is designed and characterized.

  4. Joint Decoding of Concatenated VLEC and STTC System

    Directory of Open Access Journals (Sweden)

    Chen Huijun

    2008-01-01

    Full Text Available Abstract We consider the decoding of wireless communication systems with both source coding in the application layer and channel coding in the physical layer for high-performance transmission over fading channels. Variable length error correcting codes (VLECs and space time trellis codes (STTCs are used to provide bandwidth efficient data compression as well as coding and diversity gains. At the receiver, an iterative joint source and space time decoding scheme are developed to utilize redundancy in both STTC and VLEC to improve overall decoding performance. Issues such as the inseparable systematic information in the symbol level, the asymmetric trellis structure of VLEC, and information exchange between bit and symbol domains have been considered in the maximum a posteriori probability (MAP decoding algorithm. Simulation results indicate that the developed joint decoding scheme achieves a significant decoding gain over the separate decoding in fading channels, whether or not the channel information is perfectly known at the receiver. Furthermore, how rate allocation between STTC and VLEC affects the performance of the joint source and space-time decoder is investigated. Different systems with a fixed overall information rate are studied. It is shown that for a system with more redundancy dedicated to the source code and a higher order modulation of STTC, the joint decoding yields better performance, though with increased complexity.

  5. Joint Decoding of Concatenated VLEC and STTC System

    Directory of Open Access Journals (Sweden)

    Huijun Chen

    2008-07-01

    Full Text Available We consider the decoding of wireless communication systems with both source coding in the application layer and channel coding in the physical layer for high-performance transmission over fading channels. Variable length error correcting codes (VLECs and space time trellis codes (STTCs are used to provide bandwidth efficient data compression as well as coding and diversity gains. At the receiver, an iterative joint source and space time decoding scheme are developed to utilize redundancy in both STTC and VLEC to improve overall decoding performance. Issues such as the inseparable systematic information in the symbol level, the asymmetric trellis structure of VLEC, and information exchange between bit and symbol domains have been considered in the maximum a posteriori probability (MAP decoding algorithm. Simulation results indicate that the developed joint decoding scheme achieves a significant decoding gain over the separate decoding in fading channels, whether or not the channel information is perfectly known at the receiver. Furthermore, how rate allocation between STTC and VLEC affects the performance of the joint source and space-time decoder is investigated. Different systems with a fixed overall information rate are studied. It is shown that for a system with more redundancy dedicated to the source code and a higher order modulation of STTC, the joint decoding yields better performance, though with increased complexity.

  6. Grasp movement decoding from premotor and parietal cortex.

    Science.gov (United States)

    Townsend, Benjamin R; Subasi, Erk; Scherberger, Hansjörg

    2011-10-05

    Despite recent advances in harnessing cortical motor-related activity to control computer cursors and robotic devices, the ability to decode and execute different grasping patterns remains a major obstacle. Here we demonstrate a simple Bayesian decoder for real-time classification of grip type and wrist orientation in macaque monkeys that uses higher-order planning signals from anterior intraparietal cortex (AIP) and ventral premotor cortex (area F5). Real-time decoding was based on multiunit signals, which had similar tuning properties to cells in previous single-unit recording studies. Maximum decoding accuracy for two grasp types (power and precision grip) and five wrist orientations was 63% (chance level, 10%). Analysis of decoder performance showed that grip type decoding was highly accurate (90.6%), with most errors occurring during orientation classification. In a subsequent off-line analysis, we found small but significant performance improvements (mean, 6.25 percentage points) when using an optimized spike-sorting method (superparamagnetic clustering). Furthermore, we observed significant differences in the contributions of F5 and AIP for grasp decoding, with F5 being better suited for classification of the grip type and AIP contributing more toward decoding of object orientation. However, optimum decoding performance was maximal when using neural activity simultaneously from both areas. Overall, these results highlight quantitative differences in the functional representation of grasp movements in AIP and F5 and represent a first step toward using these signals for developing functional neural interfaces for hand grasping.

  7. Efficient Decoding of Partial Unit Memory Codes of Arbitrary Rate

    CERN Document Server

    Wachter-Zeh, Antonia; Bossert, Martin

    2012-01-01

    Partial Unit Memory (PUM) codes are a special class of convolutional codes, which are often constructed by means of block codes. Decoding of PUM codes may take advantage of existing decoders for the block code. The Dettmar--Sorger algorithm is an efficient decoding algorithm for PUM codes, but allows only low code rates. The same restriction holds for several known PUM code constructions. In this paper, an arbitrary-rate construction, the analysis of its distance parameters and a generalized decoding algorithm for PUM codes of arbitrary rate are provided. The correctness of the algorithm is proven and it is shown that its complexity is cubic in the length.

  8. On Rational Interpolation-Based List-Decoding and List-Decoding Binary Goppa Codes

    DEFF Research Database (Denmark)

    Beelen, Peter; Høholdt, Tom; Nielsen, Johan Sebastian Rosenkilde;

    2013-01-01

    We derive the Wu list-decoding algorithm for generalized Reed–Solomon (GRS) codes by using Gröbner bases over modules and the Euclidean algorithm as the initial algorithm instead of the Berlekamp–Massey algorithm. We present a novel method for constructing the interpolation polynomial fast. We give...

  9. A primer on equalization, decoding and non-iterative joint equalization and decoding

    Science.gov (United States)

    Myburgh, Hermanus C.; Olivier, Jan C.

    2013-12-01

    In this article, a general model for non-iterative joint equalization and decoding is systematically derived for use in systems transmitting convolutionally encoded BPSK-modulated information through a multipath channel, with and without interleaving. Optimal equalization and decoding are discussed first, by presenting the maximum likelihood sequence estimation and maximum a posteriori probability algorithms and relating them to equalization in single-carrier channels with memory, and to the decoding of convolutional codes. The non-iterative joint equalizer/decoder (NI-JED) is then derived for the case where no interleaver is used, as well as for the case when block interleavers of varying depths are used, and complexity analyses are performed in each case. Simulation results are performed to compare the performance of the NI-JED to that of a conventional turbo equalizer (CTE), and it is shown that the NI-JED outperforms the CTE, although at much higher computational cost. This article serves to explain the state-of-the-art to students and professionals in the field of wireless communication systems, presenting these fundamental topics clearly and concisely.

  10. Beyond Discovery

    DEFF Research Database (Denmark)

    Korsgaard, Steffen; Sassmannshausen, Sean Patrick

    2015-01-01

    as their central concepts and conceptualization of the entrepreneurial function. On this basis we discuss three central themes that cut across the four alternatives: process, uncertainty, and agency. These themes provide new foci for entrepreneurship research and can help to generate new research questions......In this chapter we explore four alternatives to the dominant discovery view of entrepreneurship; the development view, the construction view, the evolutionary view, and the Neo-Austrian view. We outline the main critique points of the discovery presented in these four alternatives, as well...

  11. Neural decoding reveals impaired face configural processing in the right fusiform face area of individuals with developmental prosopagnosia.

    Science.gov (United States)

    Zhang, Jiedong; Liu, Jia; Xu, Yaoda

    2015-01-28

    Most of human daily social interactions rely on the ability to successfully recognize faces. Yet ∼2% of the human population suffers from face blindness without any acquired brain damage [this is also known as developmental prosopagnosia (DP) or congenital prosopagnosia]). Despite the presence of severe behavioral face recognition deficits, surprisingly, a majority of DP individuals exhibit normal face selectivity in the right fusiform face area (FFA), a key brain region involved in face configural processing. This finding, together with evidence showing impairments downstream from the right FFA in DP individuals, has led some to argue that perhaps the right FFA is largely intact in DP individuals. Using fMRI multivoxel pattern analysis, here we report the discovery of a neural impairment in the right FFA of DP individuals that may play a critical role in mediating their face-processing deficits. In seven individuals with DP, we discovered that, despite the right FFA's preference for faces and it showing decoding for the different face parts, it exhibited impaired face configural decoding and did not contain distinct neural response patterns for the intact and the scrambled face configurations. This abnormality was not present throughout the ventral visual cortex, as normal neural decoding was found in an adjacent object-processing region. To our knowledge, this is the first direct neural evidence showing impaired face configural processing in the right FFA in individuals with DP. The discovery of this neural impairment provides a new clue to our understanding of the neural basis of DP.

  12. Maximum a posteriori decoder for digital communications

    Science.gov (United States)

    Altes, Richard A. (Inventor)

    1997-01-01

    A system and method for decoding by identification of the most likely phase coded signal corresponding to received data. The present invention has particular application to communication with signals that experience spurious random phase perturbations. The generalized estimator-correlator uses a maximum a posteriori (MAP) estimator to generate phase estimates for correlation with incoming data samples and for correlation with mean phases indicative of unique hypothesized signals. The result is a MAP likelihood statistic for each hypothesized transmission, wherein the highest value statistic identifies the transmitted signal.

  13. GLRT-Optimal Noncoherent Lattice Decoding

    CERN Document Server

    Ryan, Daniel J; Clarkson, I Vaughan L

    2007-01-01

    This paper presents new low-complexity lattice-decoding algorithms for noncoherent block detection of QAM and PAM signals over complex-valued fading channels. The algorithms are optimal in terms of the generalized likelihood ratio test (GLRT). The computational complexity is polynomial in the block length; making GLRT-optimal noncoherent detection feasible for implementation. We also provide even lower complexity suboptimal algorithms. Simulations show that the suboptimal algorithms have performance indistinguishable from the optimal algorithms. Finally, we consider block based transmission, and propose to use noncoherent detection as an alternative to pilot assisted transmission (PAT). The new technique is shown to outperform PAT.

  14. Word Processing in Dyslexics: An Automatic Decoding Deficit?

    Science.gov (United States)

    Yap, Regina; Van Der Leu, Aryan

    1993-01-01

    Compares dyslexic children with normal readers on measures of phonological decoding and automatic word processing. Finds that dyslexics have a deficit in automatic phonological decoding skills. Discusses results within the framework of the phonological deficit and the automatization deficit hypotheses. (RS)

  15. A Method of Coding and Decoding in Underwater Image Transmission

    Institute of Scientific and Technical Information of China (English)

    程恩

    2001-01-01

    A new method of coding and decoding in the system of underwater image transmission is introduced, including the rapid digital frequency synthesizer in multiple frequency shift keying,image data generator, image grayscale decoder with intelligent fuzzy algorithm, image restoration and display on microcomputer.

  16. Interim Manual for the DST: Decoding Skills Test.

    Science.gov (United States)

    Richardson, Ellis; And Others

    The Decoding Skills Test (DST) was developed to provide a detailed measurement of decoding skills which could be used in research on developmental dyslexia. Another purpose of the test is to provide a diagnostic-prescriptive instrument to be used in the evaluation of, and program planning for, children needing remedial reading. The test is…

  17. A VLSI design for a trace-back Viterbi decoder

    Science.gov (United States)

    Truong, T. K.; Shih, Ming-Tang; Reed, Irving S.; Satorius, E. H.

    1992-01-01

    A systolic Viterbi decoder for convolutional codes is developed which uses the trace-back method to reduce the amount of data needed to be stored in registers. It is shown that this new algorithm requires a smaller chip size and achieves a faster decoding time than other existing methods.

  18. LDPC Codes--Structural Analysis and Decoding Techniques

    Science.gov (United States)

    Zhang, Xiaojie

    2012-01-01

    Low-density parity-check (LDPC) codes have been the focus of much research over the past decade thanks to their near Shannon limit performance and to their efficient message-passing (MP) decoding algorithms. However, the error floor phenomenon observed in MP decoding, which manifests itself as an abrupt change in the slope of the error-rate curve,…

  19. Socialization Processes in Encoding and Decoding: Learning Effective Nonverbal Behavior.

    Science.gov (United States)

    Feldman, Robert S.; Coats, Erik

    This study examined the relationship of nonverbal encoding and decoding skills to the level of exposure to television. Subjects were children in second through sixth grade. Three nonverbal skills (decoding, spontaneous encoding, and posed encoding) were assessed for each of five emotions: anger, disgust, fear or surprise, happiness, and sadness.…

  20. Decoding Information in the Human Hippocampus: A User's Guide

    Science.gov (United States)

    Chadwick, Martin J.; Bonnici, Heidi M.; Maguire, Eleanor A.

    2012-01-01

    Multi-voxel pattern analysis (MVPA), or "decoding", of fMRI activity has gained popularity in the neuroimaging community in recent years. MVPA differs from standard fMRI analyses by focusing on whether information relating to specific stimuli is encoded in patterns of activity across multiple voxels. If a stimulus can be predicted, or decoded,…

  1. 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....

  2. Building Bridges from the Decoding Interview to Teaching Practice

    Science.gov (United States)

    Pettit, Jennifer; Rathburn, Melanie; Calvert, Victoria; Lexier, Roberta; Underwood, Margot; Gleeson, Judy; Dean, Yasmin

    2017-01-01

    This chapter describes a multidisciplinary faculty self-study about reciprocity in service-learning. The study began with each coauthor participating in a Decoding interview. We describe how Decoding combined with collaborative self-study had a positive impact on our teaching practice.

  3. Decoding Technique of Concatenated Hadamard Codes and Its Performance

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    The decoding technique of concatenated Hadamard codes and its performance are studied. Efficient softin-soft-out decoding algorithms based on the fast Hadamard transform are developed. Performance required by CDMA mobile or PCS speech services, e.g. , BER= 10-3, can be achieved at Eb/No = 0.9 dB using short interleaving length of 192 bits.

  4. Latent state-space models for neural decoding.

    Science.gov (United States)

    Aghagolzadeh, Mehdi; Truccolo, Wilson

    2014-01-01

    Ensembles of single-neurons in motor cortex can show strong low-dimensional collective dynamics. In this study, we explore an approach where neural decoding is applied to estimated low-dimensional dynamics instead of to the full recorded neuronal population. A latent state-space model (SSM) approach is used to estimate the low-dimensional neural dynamics from the measured spiking activity in population of neurons. A second state-space model representation is then used to decode kinematics, via a Kalman filter, from the estimated low-dimensional dynamics. The latent SSM-based decoding approach is illustrated on neuronal activity recorded from primary motor cortex in a monkey performing naturalistic 3-D reach and grasp movements. Our analysis show that 3-D reach decoding performance based on estimated low-dimensional dynamics is comparable to the decoding performance based on the full recorded neuronal population.

  5. An efficient VLSI implementation of H.264/AVC entropy decoder

    Institute of Scientific and Technical Information of China (English)

    Jongsik; PARK; Jeonhak; MOON; Seongsoo; LEE

    2010-01-01

    <正>This paper proposes an efficient H.264/AVC entropy decoder.It requires no ROM/RAM fabrication process that decreases fabrication cost and increases operation speed.It was achieved by optimizing lookup tables and internal buffers,which significantly improves area,speed,and power.The proposed entropy decoder does not exploit embedded processor for bitstream manipulation, which also improves area,speed,and power.Its gate counts and maximum operation frequency are 77515 gates and 175MHz in 0.18um fabrication process,respectively.The proposed entropy decoder needs 2303 cycles in average for one macroblock decoding.It can run at 28MHz to meet the real-time processing requirement for CIF format video decoding on mobile applications.

  6. EEG source imaging assists decoding in a face recognition task

    DEFF Research Database (Denmark)

    Andersen, Rasmus S.; Eliasen, Anders U.; Pedersen, Nicolai

    2017-01-01

    EEG based brain state decoding has numerous applications. State of the art decoding is based on processing of the multivariate sensor space signal, however evidence is mounting that EEG source reconstruction can assist decoding. EEG source imaging leads to high-dimensional representations...... of face recognition. This task concerns the differentiation of brain responses to images of faces and scrambled faces and poses a rather difficult decoding problem at the single trial level. We implement the pipeline using spatially focused features and show that this approach is challenged and source...... imaging does not lead to an improved decoding. We design a distributed pipeline in which the classifier has access to brain wide features which in turn does lead to a 15% reduction in the error rate using source space features. Hence, our work presents supporting evidence for the hypothesis that source...

  7. FPGA Prototyping of RNN Decoder for Convolutional Codes

    Directory of Open Access Journals (Sweden)

    Salcic Zoran

    2006-01-01

    Full Text Available This paper presents prototyping of a recurrent type neural network (RNN convolutional decoder using system-level design specification and design flow that enables easy mapping to the target FPGA architecture. Implementation and the performance measurement results have shown that an RNN decoder for hard-decision decoding coupled with a simple hard-limiting neuron activation function results in a very low complexity, which easily fits into standard Altera FPGA. Moreover, the design methodology allowed modeling of complete testbed for prototyping RNN decoders in simulation and real-time environment (same FPGA, thus enabling evaluation of BER performance characteristics of the decoder for various conditions of communication channel in real time.

  8. Iterative List Decoding of Concatenated Source-Channel Codes

    Directory of Open Access Journals (Sweden)

    Hedayat Ahmadreza

    2005-01-01

    Full Text Available Whenever variable-length entropy codes are used in the presence of a noisy channel, any channel errors will propagate and cause significant harm. Despite using channel codes, some residual errors always remain, whose effect will get magnified by error propagation. Mitigating this undesirable effect is of great practical interest. One approach is to use the residual redundancy of variable length codes for joint source-channel decoding. In this paper, we improve the performance of residual redundancy source-channel decoding via an iterative list decoder made possible by a nonbinary outer CRC code. We show that the list decoding of VLC's is beneficial for entropy codes that contain redundancy. Such codes are used in state-of-the-art video coders, for example. The proposed list decoder improves the overall performance significantly in AWGN and fully interleaved Rayleigh fading channels.

  9. Multi-stage decoding of multi-level modulation codes

    Science.gov (United States)

    Lin, Shu; Kasami, Tadao; Costello, Daniel J., Jr.

    1991-01-01

    Various types of multi-stage decoding for multi-level modulation codes are investigated. It is shown that if the component codes of a multi-level modulation code and types of decoding at various stages are chosen properly, high spectral efficiency and large coding gain can be achieved with reduced decoding complexity. Particularly, it is shown that the difference in performance between the suboptimum multi-stage soft-decision maximum likelihood decoding of a modulation code and the single-stage optimum soft-decision decoding of the code is very small, only a fraction of dB loss in signal to noise ratio at a bit error rate (BER) of 10(exp -6).

  10. Multilevel Decoders Surpassing Belief Propagation on the Binary Symmetric Channel

    CERN Document Server

    Planjery, Shiva Kumar; Chilappagari, Shashi Kiran; Vasić, Bane

    2010-01-01

    In this paper, we propose a new class of quantized message-passing decoders for LDPC codes over the BSC. The messages take values (or levels) from a finite set. The update rules do not mimic belief propagation but instead are derived using the knowledge of trapping sets. We show that the update rules can be derived to correct certain error patterns that are uncorrectable by algorithms such as BP and min-sum. In some cases even with a small message set, these decoders can guarantee correction of a higher number of errors than BP and min-sum. We provide particularly good 3-bit decoders for 3-left-regular LDPC codes. They significantly outperform the BP and min-sum decoders, but more importantly, they achieve this at only a fraction of the complexity of the BP and min-sum decoders.

  11. Improved decoding of limb-state feedback from natural sensors.

    Science.gov (United States)

    Wagenaar, J B; Ventura, V; Weber, D J

    2009-01-01

    Limb state feedback is of great importance for achieving stable and adaptive control of FES neuroprostheses. A natural way to determine limb state is to measure and decode the activity of primary afferent neurons in the limb. The feasibility of doing so has been demonstrated by [1] and [2]. Despite positive results, some drawbacks in these works are associated with the application of reverse regression techniques for decoding the afferent neuronal signals. Decoding methods that are based on direct regression are now favored over reverse regression for decoding neural responses in higher regions in the central nervous system [3]. In this paper, we apply a direct regression approach to decode the movement of the hind limb of a cat from a population of primary afferent neurons. We show that this approach is more principled, more efficient, and more generalizable than reverse regression.

  12. Lattice Sequential Decoder for Coded MIMO Channel: Performance and Complexity Analysis

    CERN Document Server

    Abediseid, Walid

    2011-01-01

    In this paper, the performance limit of lattice sequential decoder for lattice space-time coded MIMO channel is analysed. We determine the rates achievable by lattice coding and sequential decoding applied to such channel. The diversity-multiplexing tradeoff (DMT) under lattice sequential decoding is derived as a function of its parameter---the bias term. The bias parameter is critical for controlling the amount of computations required at the decoding stage. Achieving low decoding complexity requires increasing the value of the bias term. However, this is done at the expense of losing the optimal tradeoff of the channel. We show how such a decoder can bridge the gap between lattice decoder and low complexity decoders. Moreover, the computational complexity of lattice sequential decoder is analysed. Specifically, we derive the tail distribution of the decoder's computational complexity in the high signal-to-noise ratio regime. Similar to the conventional sequential decoder used in discrete memoryless channel,...

  13. Decoding suprathreshold stochastic resonance with optimal weights

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Liyan, E-mail: xuliyan@qdu.edu.cn [Institute of Complexity Science, Qingdao University, Qingdao 266071 (China); Vladusich, Tony [Computational and Theoretical Neuroscience Laboratory, Institute for Telecommunications Research, School of Information Technology and Mathematical Sciences, University of South Australia, SA 5095 (Australia); Duan, Fabing [Institute of Complexity Science, Qingdao University, Qingdao 266071 (China); Gunn, Lachlan J.; Abbott, Derek [Centre for Biomedical Engineering (CBME) and School of Electrical & Electronic Engineering, The University of Adelaide, Adelaide, SA 5005 (Australia); McDonnell, Mark D. [Computational and Theoretical Neuroscience Laboratory, Institute for Telecommunications Research, School of Information Technology and Mathematical Sciences, University of South Australia, SA 5095 (Australia); Centre for Biomedical Engineering (CBME) and School of Electrical & Electronic Engineering, The University of Adelaide, Adelaide, SA 5005 (Australia)

    2015-10-09

    We investigate an array of stochastic quantizers for converting an analog input signal into a discrete output in the context of suprathreshold stochastic resonance. A new optimal weighted decoding is considered for different threshold level distributions. We show that for particular noise levels and choices of the threshold levels optimally weighting the quantizer responses provides a reduced mean square error in comparison with the original unweighted array. However, there are also many parameter regions where the original array provides near optimal performance, and when this occurs, it offers a much simpler approach than optimally weighting each quantizer's response. - Highlights: • A weighted summing array of independently noisy binary comparators is investigated. • We present an optimal linearly weighted decoding scheme for combining the comparator responses. • We solve for the optimal weights by applying least squares regression to simulated data. • We find that the MSE distortion of weighting before summation is superior to unweighted summation of comparator responses. • For some parameter regions, the decrease in MSE distortion due to weighting is negligible.

  14. Implementation of Huffman Decoder on Fpga

    Directory of Open Access Journals (Sweden)

    Safia Amir Dahri

    2016-01-01

    Full Text Available Lossless data compression algorithm is most widely used algorithm in data transmission, reception and storage systems in order to increase data rate, speed and save lots of space on storage devices. Now-a-days, different algorithms are implemented in hardware to achieve benefits of hardware realizations. Hardware implementation of algorithms, digital signal processing algorithms and filter realization is done on programmable devices i.e. FPGA. In lossless data compression algorithms, Huffman algorithm is most widely used because of its variable length coding features and many other benefits. Huffman algorithms are used in many applications in software form, e.g. Zip and Unzip, communication, etc. In this paper, Huffman algorithm is implemented on Xilinx Spartan 3E board. This FPGA is programmed by Xilinx tool, Xilinx ISE 8.2i. The program is written in VHDL and text data is decoded by a Huffman algorithm on Hardware board which was previously encoded by Huffman algorithm. In order to visualize the output clearly in waveforms, the same code is simulated on ModelSim v6.4. Huffman decoder is also implemented in the MATLAB for verification of operation. The FPGA is a configurable device which is more efficient in all aspects. Text application, image processing, video streaming and in many other applications Huffman algorithms are implemented.

  15. SDRAM bus schedule of HDTV video decoder

    Science.gov (United States)

    Wang, Hui; He, Yan L.; Yu, Lu

    2001-12-01

    In this paper, a time division multiplexed task scheduling (TDM) is designed for HDTV video decoder is proposed. There are three tasks: to fetch decoded data from SDRAM for displaying (DIS), read the reference data from SDRAM for motion compensating (REF) and write the motion compensated data back to SDRAM (WB) on the bus. The proposed schedule is based on the novel 4 banks interlaced SDRAM storage structure which results in less overhead on read/write time. Two SDRAM of 64M bits (4Bank×512K×32bit) are used. Compared with two banks, the four banks storage strategy read/write data with 45% less time. Therefore the process data rates for those three tasks are reduced. TDM is developed by round robin scheduling and fixed slot allocating. There are both MB slot and task slot. As a result the conflicts on bus are avoided, and the buffer size is reduced 48% compared with the priority bus scheduling. Moreover, there is a compacted bus schedule for the worst case of stuffing owning to the reduced executing time on tasks. The size of buffer is reduced and the control logic is simplified.

  16. The Differential Contributions of Auditory-Verbal and Visuospatial Working Memory on Decoding Skills in Children Who Are Poor Decoders

    Science.gov (United States)

    Squires, Katie Ellen

    2013-01-01

    This study investigated the differential contribution of auditory-verbal and visuospatial working memory (WM) on decoding skills in second- and fifth-grade children identified with poor decoding. Thirty-two second-grade students and 22 fifth-grade students completed measures that assessed simple and complex auditory-verbal and visuospatial memory,…

  17. Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison.

    Science.gov (United States)

    Kazemian, Majid; Zhu, Qiyun; Halfon, Marc S; Sinha, Saurabh

    2011-12-01

    Despite recent advances in experimental approaches for identifying transcriptional cis-regulatory modules (CRMs, 'enhancers'), direct empirical discovery of CRMs for all genes in all cell types and environmental conditions is likely to remain an elusive goal. Effective methods for computational CRM discovery are thus a critically needed complement to empirical approaches. However, existing computational methods that search for clusters of putative binding sites are ineffective if the relevant TFs and/or their binding specificities are unknown. Here, we provide a significantly improved method for 'motif-blind' CRM discovery that does not depend on knowledge or accurate prediction of TF-binding motifs and is effective when limited knowledge of functional CRMs is available to 'supervise' the search. We propose a new statistical method, based on 'Interpolated Markov Models', for motif-blind, genome-wide CRM discovery. It captures the statistical profile of variable length words in known CRMs of a regulatory network and finds candidate CRMs that match this profile. The method also uses orthologs of the known CRMs from closely related genomes. We perform in silico evaluation of predicted CRMs by assessing whether their neighboring genes are enriched for the expected expression patterns. This assessment uses a novel statistical test that extends the widely used Hypergeometric test of gene set enrichment to account for variability in intergenic lengths. We find that the new CRM prediction method is superior to existing methods. Finally, we experimentally validate 12 new CRM predictions by examining their regulatory activity in vivo in Drosophila; 10 of the tested CRMs were found to be functional, while 6 of the top 7 predictions showed the expected activity patterns. We make our program available as downloadable source code, and as a plugin for a genome browser installed on our servers.

  18. Encoder-decoder optimization for brain-computer interfaces.

    Directory of Open Access Journals (Sweden)

    Josh Merel

    2015-06-01

    Full Text Available Neuroprosthetic brain-computer interfaces are systems that decode neural activity into useful control signals for effectors, such as a cursor on a computer screen. It has long been recognized that both the user and decoding system can adapt to increase the accuracy of the end effector. Co-adaptation is the process whereby a user learns to control the system in conjunction with the decoder adapting to learn the user's neural patterns. We provide a mathematical framework for co-adaptation and relate co-adaptation to the joint optimization of the user's control scheme ("encoding model" and the decoding algorithm's parameters. When the assumptions of that framework are respected, co-adaptation cannot yield better performance than that obtainable by an optimal initial choice of fixed decoder, coupled with optimal user learning. For a specific case, we provide numerical methods to obtain such an optimized decoder. We demonstrate our approach in a model brain-computer interface system using an online prosthesis simulator, a simple human-in-the-loop pyschophysics setup which provides a non-invasive simulation of the BCI setting. These experiments support two claims: that users can learn encoders matched to fixed, optimal decoders and that, once learned, our approach yields expected performance advantages.

  19. On decoding of multi-level MPSK modulation codes

    Science.gov (United States)

    Lin, Shu; Gupta, Alok Kumar

    1990-01-01

    The decoding problem of multi-level block modulation codes is investigated. The hardware design of soft-decision Viterbi decoder for some short length 8-PSK block modulation codes is presented. An effective way to reduce the hardware complexity of the decoder by reducing the branch metric and path metric, using a non-uniform floating-point to integer mapping scheme, is proposed and discussed. The simulation results of the design are presented. The multi-stage decoding (MSD) of multi-level modulation codes is also investigated. The cases of soft-decision and hard-decision MSD are considered and their performance are evaluated for several codes of different lengths and different minimum squared Euclidean distances. It is shown that the soft-decision MSD reduces the decoding complexity drastically and it is suboptimum. The hard-decision MSD further simplifies the decoding while still maintaining a reasonable coding gain over the uncoded system, if the component codes are chosen properly. Finally, some basic 3-level 8-PSK modulation codes using BCH codes as component codes are constructed and their coding gains are found for hard decision multistage decoding.

  20. Hard decoding algorithm for optimizing thresholds under general Markovian noise

    Science.gov (United States)

    Chamberland, Christopher; Wallman, Joel; Beale, Stefanie; Laflamme, Raymond

    2017-04-01

    Quantum error correction is instrumental in protecting quantum systems from noise in quantum computing and communication settings. Pauli channels can be efficiently simulated and threshold values for Pauli error rates under a variety of error-correcting codes have been obtained. However, realistic quantum systems can undergo noise processes that differ significantly from Pauli noise. In this paper, we present an efficient hard decoding algorithm for optimizing thresholds and lowering failure rates of an error-correcting code under general completely positive and trace-preserving (i.e., Markovian) noise. We use our hard decoding algorithm to study the performance of several error-correcting codes under various non-Pauli noise models by computing threshold values and failure rates for these codes. We compare the performance of our hard decoding algorithm to decoders optimized for depolarizing noise and show improvements in thresholds and reductions in failure rates by several orders of magnitude. Our hard decoding algorithm can also be adapted to take advantage of a code's non-Pauli transversal gates to further suppress noise. For example, we show that using the transversal gates of the 5-qubit code allows arbitrary rotations around certain axes to be perfectly corrected. Furthermore, we show that Pauli twirling can increase or decrease the threshold depending upon the code properties. Lastly, we show that even if the physical noise model differs slightly from the hypothesized noise model used to determine an optimized decoder, failure rates can still be reduced by applying our hard decoding algorithm.

  1. Approximate Decoding Approaches for Network Coded Correlated Data

    CERN Document Server

    Park, Hyunggon; Frossard, Pascal

    2011-01-01

    This paper considers a framework where data from correlated sources are transmitted with help of network coding in ad-hoc network topologies. The correlated data are encoded independently at sensors and network coding is employed in the intermediate nodes in order to improve the data delivery performance. In such settings, we focus on the problem of reconstructing the sources at decoder when perfect decoding is not possible due to losses or bandwidth bottlenecks. We first show that the source data similarity can be used at decoder to permit decoding based on a novel and simple approximate decoding scheme. We analyze the influence of the network coding parameters and in particular the size of finite coding fields on the decoding performance. We further determine the optimal field size that maximizes the expected decoding performance as a trade-off between information loss incurred by limiting the resolution of the source data and the error probability in the reconstructed data. Moreover, we show that the perfo...

  2. On Multiple Decoding Attempts for Reed-Solomon Codes

    CERN Document Server

    Nguyen, Phong S; Narayanan, Krishna R

    2010-01-01

    One popular approach to soft-decision decoding of Reed-Solomon (RS) codes is based on the idea of using multiple trials of a simple RS decoding algorithm in combination with successively erasing or flipping a set of symbols or bits in each trial. In this paper, we present an framework based on rate-distortion (RD) theory to analyze such multiple-decoding algorithms for RS codes. By defining an appropriate distortion measure between an error pattern and an erasure pattern, it is shown that, for a single errors-and-erasures decoding trial, the condition for successful decoding is equivalent to the condition that the distortion is smaller than a fixed threshold. Finding the best set of erasure patterns for multiple decoding trials then turns out to be a covering problem which can be solved asymptotically by rate-distortion theory. Thus, the proposed approach can be used to understand the asymptotic performance-versus-complexity trade-off of multiple errors-and-erasures decoding of RS codes. We also consider an a...

  3. O2-GIDNC: Beyond instantly decodable network coding

    KAUST Repository

    Aboutorab, Neda

    2013-06-01

    In this paper, we are concerned with extending the graph representation of generalized instantly decodable network coding (GIDNC) to a more general opportunistic network coding (ONC) scenario, referred to as order-2 GIDNC (O2-GIDNC). In the O2-GIDNC scheme, receivers can store non-instantly decodable packets (NIDPs) comprising two of their missing packets, and use them in a systematic way for later decodings. Once this graph representation is found, it can be used to extend the GIDNC graph-based analyses to the proposed O2-GIDNC scheme with a limited increase in complexity. In the proposed O2-GIDNC scheme, the information of the stored NIDPs at the receivers and the decoding opportunities they create can be exploited to improve the broadcast completion time and decoding delay compared to traditional GIDNC scheme. The completion time and decoding delay minimizing algorithms that can operate on the new O2-GIDNC graph are further described. The simulation results show that our proposed O2-GIDNC improves the completion time and decoding delay performance of the traditional GIDNC. © 2013 IEEE.

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

    CERN Document Server

    Senger, Christian; Bossert, Martin; Zyablov, Victor

    2008-01-01

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

  5. Coding and Decoding for the Dynamic Decode and Forward Relay Protocol

    CERN Document Server

    Kumar, K Raj

    2008-01-01

    We study the Dynamic Decode and Forward (DDF) protocol for a single half-duplex relay, single-antenna channel with quasi-static fading. The DDF protocol is well-known and has been analyzed in terms of the Diversity-Multiplexing Tradeoff (DMT) in the infinite block length limit. We characterize the finite block length DMT and give new explicit code constructions. The finite block length analysis illuminates a few key aspects that have been neglected in the previous literature: 1) we show that one dominating cause of degradation with respect to the infinite block length regime is the event of decoding error at the relay; 2) we explicitly take into account the fact that the destination does not generally know a priori the relay decision time at which the relay switches from listening to transmit mode. Both the above problems can be tackled by a careful design of the decoding algorithm. In particular, we introduce a decision rejection criterion at the relay based on Forney's decision rule (a variant of the Neyman...

  6. Decoding the mechanisms of Antikythera astronomical device

    CERN Document Server

    Lin, Jian-Liang

    2016-01-01

    This book presents a systematic design methodology for decoding the interior structure of the Antikythera mechanism, an astronomical device from ancient Greece. The historical background, surviving evidence and reconstructions of the mechanism are introduced, and the historical development of astronomical achievements and various astronomical instruments are investigated. Pursuing an approach based on the conceptual design of modern mechanisms and bearing in mind the standards of science and technology at the time, all feasible designs of the six lost/incomplete/unclear subsystems are synthesized as illustrated examples, and 48 feasible designs of the complete interior structure are presented. This approach provides not only a logical tool for applying modern mechanical engineering knowledge to the reconstruction of the Antikythera mechanism, but also an innovative research direction for identifying the original structures of the mechanism in the future. In short, the book offers valuable new insights for all...

  7. Interference Alignment for Clustered Multicell Joint Decoding

    CERN Document Server

    Chatzinotas, Symeon

    2010-01-01

    Multicell joint processing has been proven to be very efficient in overcoming the interference-limited nature of the cellular paradigm. However, for reasons of practical implementation global multicell joint decoding is not feasible and thus clusters of cooperating Base Stations have to be considered. In this context, intercluster interference has to be mitigated in order to harvest the full potential of multicell joint processing. In this paper, four scenarios of intercluster interference are investigated, namely a) global multicell joint processing, b) interference alignment, c) resource division multiple access and d) cochannel interference allowance. Each scenario is modelled and analyzed using the per-cell ergodic sum-rate capacity as a figure of merit. In this process, a number of theorems are derived for analytically expressing the asymptotic eigenvalue distributions of the channel covariance matrices. The analysis is based on principles from Free Probability theory and especially properties in the R a...

  8. Real-time minimal bit error probability decoding of convolutional codes

    Science.gov (United States)

    Lee, L. N.

    1973-01-01

    A recursive procedure is derived for decoding of rate R=1/n binary convolutional codes which minimizes the probability of the individual decoding decisions for each information bit subject to the constraint that the decoding delay be limited to Delta branches. This new decoding algorithm is similar to, but somewhat more complex than, the Viterbi decoding algorithm. A real-time, i.e. fixed decoding delay, version of the Viterbi algorithm is also developed and used for comparison to the new algorithm on simulated channels. It is shown that the new algorithm offers advantages over Viterbi decoding in soft-decision applications such as in the inner coding system for concatenated coding.

  9. Real-time minimal-bit-error probability decoding of convolutional codes

    Science.gov (United States)

    Lee, L.-N.

    1974-01-01

    A recursive procedure is derived for decoding of rate R = 1/n binary convolutional codes which minimizes the probability of the individual decoding decisions for each information bit, subject to the constraint that the decoding delay be limited to Delta branches. This new decoding algorithm is similar to, but somewhat more complex than, the Viterbi decoding algorithm. A real-time, i.e., fixed decoding delay, version of the Viterbi algorithm is also developed and used for comparison to the new algorithm on simulated channels. It is shown that the new algorithm offers advantages over Viterbi decoding in soft-decision applications, such as in the inner coding system for concatenated coding.

  10. Locally decodable codes and private information retrieval schemes

    CERN Document Server

    Yekhanin, Sergey

    2010-01-01

    Locally decodable codes (LDCs) are codes that simultaneously provide efficient random access retrieval and high noise resilience by allowing reliable reconstruction of an arbitrary bit of a message by looking at only a small number of randomly chosen codeword bits. Local decodability comes with a certain loss in terms of efficiency - specifically, locally decodable codes require longer codeword lengths than their classical counterparts. Private information retrieval (PIR) schemes are cryptographic protocols designed to safeguard the privacy of database users. They allow clients to retrieve rec

  11. Turbo decoder architecture for beyond-4G applications

    CERN Document Server

    Wong, Cheng-Chi

    2013-01-01

    This book describes the most recent techniques for turbo decoder implementation, especially for 4G and beyond 4G applications. The authors reveal techniques for the design of high-throughput decoders for future telecommunication systems, enabling designers to reduce hardware cost and shorten processing time. Coverage includes an explanation of VLSI implementation of the turbo decoder, from basic functional units to advanced parallel architecture. The authors discuss both hardware architecture techniques and experimental results, showing the variations in area/throughput/performance with respec

  12. 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...

  13. Analysis and Design of Binary Message-Passing Decoders

    DEFF Research Database (Denmark)

    Lechner, Gottfried; Pedersen, Troels; Kramer, Gerhard

    2012-01-01

    Binary message-passing decoders for low-density parity-check (LDPC) codes are studied by using extrinsic information transfer (EXIT) charts. The channel delivers hard or soft decisions and the variable node decoder performs all computations in the L-value domain. A hard decision channel results...... message-passing decoders. Finally, it is shown that errors on cycles consisting only of degree two and three variable nodes cannot be corrected and a necessary and sufficient condition for the existence of a cycle-free subgraph is derived....

  14. Min-Max decoding for non binary LDPC codes

    CERN Document Server

    Savin, Valentin

    2008-01-01

    Iterative decoding of non-binary LDPC codes is currently performed using either the Sum-Product or the Min-Sum algorithms or slightly different versions of them. In this paper, several low-complexity quasi-optimal iterative algorithms are proposed for decoding non-binary codes. The Min-Max algorithm is one of them and it has the benefit of two possible LLR domain implementations: a standard implementation, whose complexity scales as the square of the Galois field's cardinality and a reduced complexity implementation called selective implementation, which makes the Min-Max decoding very attractive for practical purposes.

  15. Fast-Group-Decodable STBCs via Codes over GF(4)

    CERN Document Server

    Prasad, N Lakshmi

    2010-01-01

    In this paper we construct low decoding complexity STBCs by using the Pauli matrices as linear dispersion matrices. In this case the Hurwitz-Radon orthogonality condition is shown to be easily checked by transferring the problem to $\\mathbb{F}_4$ domain. The problem of constructing low decoding complexity STBCs is shown to be equivalent to finding certain codes over $\\mathbb{F}_4$. It is shown that almost all known low complexity STBCs can be obtained by this approach. New codes are given that have the least known decoding complexity in particular ranges of rate.

  16. Discovery Mondays

    CERN Multimedia

    2003-01-01

    Many people don't realise quite how much is going on at CERN. Would you like to gain first-hand knowledge of CERN's scientific and technological activities and their many applications? Try out some experiments for yourself, or pick the brains of the people in charge? If so, then the «Lundis Découverte» or Discovery Mondays, will be right up your street. Starting on May 5th, on every first Monday of the month you will be introduced to a different facet of the Laboratory. CERN staff, non-scientists, and members of the general public, everyone is welcome. So tell your friends and neighbours and make sure you don't miss this opportunity to satisfy your curiosity and enjoy yourself at the same time. You won't have to listen to a lecture, as the idea is to have open exchange with the expert in question and for each subject to be illustrated with experiments and demonstrations. There's no need to book, as Microcosm, CERN's interactive museum, will be open non-stop from 7.30 p.m. to 9 p.m. On the first Discovery M...

  17. Interpolating and filtering decoding algorithm for convolution codes

    Directory of Open Access Journals (Sweden)

    O. O. Shpylka

    2010-01-01

    Full Text Available There has been synthesized interpolating and filtering decoding algorithm for convolution codes on maximum of a posteriori probability criterion, in which combined filtering coder state and interpolation of information signs on sliding interval are processed

  18. Evolution of Neural Computations: Mantis Shrimp and Human Color Decoding

    Directory of Open Access Journals (Sweden)

    Qasim Zaidi

    2014-10-01

    Full Text Available Mantis shrimp and primates both possess good color vision, but the neural implementation in the two species is very different, a reflection of the largely unrelated evolutionary lineages of these creatures. Mantis shrimp have scanning compound eyes with 12 classes of photoreceptors, and have evolved a system to decode color information at the front-end of the sensory stream. Primates have image-focusing eyes with three classes of cones, and decode color further along the visual-processing hierarchy. Despite these differences, we report a fascinating parallel between the computational strategies at the color-decoding stage in the brains of stomatopods and primates. Both species appear to use narrowly tuned cells that support interval decoding color identification.

  19. Evolution of neural computations: Mantis shrimp and human color decoding.

    Science.gov (United States)

    Zaidi, Qasim; Marshall, Justin; Thoen, Hanne; Conway, Bevil R

    2014-01-01

    Mantis shrimp and primates both possess good color vision, but the neural implementation in the two species is very different, a reflection of the largely unrelated evolutionary lineages of these creatures. Mantis shrimp have scanning compound eyes with 12 classes of photoreceptors, and have evolved a system to decode color information at the front-end of the sensory stream. Primates have image-focusing eyes with three classes of cones, and decode color further along the visual-processing hierarchy. Despite these differences, we report a fascinating parallel between the computational strategies at the color-decoding stage in the brains of stomatopods and primates. Both species appear to use narrowly tuned cells that support interval decoding color identification.

  20. Construction and decoding of a class of algebraic geometry codes

    DEFF Research Database (Denmark)

    Justesen, Jørn; Larsen, Knud J.; Jensen, Helge Elbrønd

    1989-01-01

    A class of codes derived from algebraic plane curves is constructed. The concepts and results from algebraic geometry that were used are explained in detail; no further knowledge of algebraic geometry is needed. Parameters, generator and parity-check matrices are given. The main result is a decod...... is a decoding algorithm which turns out to be a generalization of the Peterson algorithm for decoding BCH decoder codes......A class of codes derived from algebraic plane curves is constructed. The concepts and results from algebraic geometry that were used are explained in detail; no further knowledge of algebraic geometry is needed. Parameters, generator and parity-check matrices are given. The main result...

  1. Decoding sound level in the marmoset primary auditory cortex.

    Science.gov (United States)

    Sun, Wensheng; Marongelli, Ellisha N; Watkins, Paul V; Barbour, Dennis L

    2017-07-12

    Neurons that respond favorably to a particular sound level have been observed throughout the central auditory system, becoming steadily more common at higher processing areas. One theory about the role of these level-tuned or nonmonotonic neurons is the level-invariant encoding of sounds. To investigate this theory, we simulated various subpopulations of neurons by drawing from real primary auditory cortex (A1) neuron responses and surveyed their performance in forming different sound level representations. Pure nonmonotonic subpopulations did not provide the best level-invariant decoding; instead, mixtures of monotonic and nonmonotonic neurons provided the most accurate decoding. For level-fidelity decoding, the inclusion of nonmonotonic neurons slightly improved or did not change decoding accuracy until they constituted a high proportion. These results indicate that nonmonotonic neurons fill an encoding role complementary to, rather than alternate to, monotonic neurons. Copyright © 2016, Journal of Neurophysiology.

  2. Multiresolutional encoding and decoding in embedded image and video coders

    Science.gov (United States)

    Xiong, Zixiang; Kim, Beong-Jo; Pearlman, William A.

    1998-07-01

    We address multiresolutional encoding and decoding within the embedded zerotree wavelet (EZW) framework for both images and video. By varying a resolution parameter, one can obtain decoded images at different resolutions from one single encoded bitstream, which is already rate scalable for EZW coders. Similarly one can decode video sequences at different rates and different spatial and temporal resolutions from one bitstream. Furthermore, a layered bitstream can be generated with multiresolutional encoding, from which the higher resolution layers can be used to increase the spatial/temporal resolution of the images/video obtained from the low resolution layer. In other words, we have achieved full scalability in rate and partial scalability in space and time. This added spatial/temporal scalability is significant for emerging multimedia applications such as fast decoding, image/video database browsing, telemedicine, multipoint video conferencing, and distance learning.

  3. On Complexity, Energy- and Implementation-Efficiency of Channel Decoders

    CERN Document Server

    Kienle, Frank; Meyr, Heinrich

    2010-01-01

    Future wireless communication systems require efficient and flexible baseband receivers. Meaningful efficiency metrics are key for design space exploration to quantify the algorithmic and the implementation complexity of a receiver. Most of the current established efficiency metrics are based on counting operations, thus neglecting important issues like data and storage complexity. In this paper we introduce suitable energy and area efficiency metrics which resolve the afore-mentioned disadvantages. These are decoded information bit per energy and throughput per area unit. Efficiency metrics are assessed by various implementations of turbo decoders, LDPC decoders and convolutional decoders. New exploration methodologies are presented, which permit an appropriate benchmarking of implementation efficiency, communications performance, and flexibility trade-offs. These exploration methodologies are based on efficiency trajectories rather than a single snapshot metric as done in state-of-the-art approaches.

  4. Tracing Precept against Self-Protective Tortious Decoder

    Institute of Scientific and Technical Information of China (English)

    Jie Tian; Xin-Fang Zhang; Yi-Lin Song; Wei Xiang

    2007-01-01

    Traceability precept is a broadcast encryption technique that content suppliers can trace malicious authorized users who leak the decryption key to an unauthorized user. To protect the data from eavesdropping, the content supplier encrypts the data and broadcast the cryptograph that only its subscribers can decrypt. However, a traitor may clone his decoder and sell the pirate decoders for profits. The traitor can modify the private key and the decryption program inside the pirate decoder to avoid divulging his identity. Furthermore, some traitors may fabricate a new legal private key together that cannot be traced to the creators. So in this paper, a renewed precept is proposed to achieve both revocation at a different level of capacity in each distribution and black-box tracing against self-protective pirate decoders. The rigorous mathematical deduction shows that our algorithm possess security property.

  5. Improved List Sphere Decoder for Multiple Antenna Systems

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    An improved list sphere decoder (ILSD) is proposed based on the conventional list sphere decoder (LSD) and the reduced-complexity maximum likelihood sphere-decoding algorithm. Unlike the conventional LSD with fixed initial radius, the ILSD adopts an adaptive radius to accelerate the list construction. Characterized by low-complexity and radius-insensitivity, the proposed algorithm makes iterative joint detection and decoding more realizable in multiple-antenna systems. Simulation results show that computational savings of ILSD over LSD are more apparent with more transmit antennas or larger constellations, and with no performance degradation. Because the complexity of the ILSD algorithm almost keeps invariant with the increasing of initial radius, the BER performance can be improved by selecting a sufficiently large radius.

  6. Low ML Decoding Complexity STBCs via Codes over GF(4)

    CERN Document Server

    Natarajan, Lakshmi Prasad

    2010-01-01

    In this paper, we give a new framework for constructing low ML decoding complexity Space-Time Block Codes (STBCs) using codes over the finite field $\\mathbb{F}_4$. Almost all known low ML decoding complexity STBCs can be obtained via this approach. New full-diversity STBCs with low ML decoding complexity and cubic shaping property are constructed, via codes over $\\mathbb{F}_4$, for number of transmit antennas \\mbox{$N=2^m$}, \\mbox{$m \\geq 1$}, and rates \\mbox{$R>1$} complex symbols per channel use. When \\mbox{$R=N$}, the new STBCs are information-lossless as well. The new class of STBCs have the least known ML decoding complexity among all the codes available in the literature for a large set of \\mbox{$(N,R)$} pairs.

  7. Decoding of visual attention from LFP signals of macaque MT.

    Science.gov (United States)

    Esghaei, Moein; Daliri, Mohammad Reza

    2014-01-01

    The local field potential (LFP) has recently been widely used in brain computer interfaces (BCI). Here we used power of LFP recorded from area MT of a macaque monkey to decode where the animal covertly attended. Support vector machines (SVM) were used to learn the pattern of power at different frequencies for attention to two possible positions. We found that LFP power at both low (<9 Hz) and high (31-120 Hz) frequencies contains sufficient information to decode the focus of attention. Highest decoding performance was found for gamma frequencies (31-120 Hz) and reached 82%. In contrast low frequencies (<9 Hz) could help the classifier reach a higher decoding performance with a smaller amount of training data. Consequently, we suggest that low frequency LFP can provide fast but coarse information regarding the focus of attention, while higher frequencies of the LFP deliver more accurate but less timely information about the focus of attention.

  8. Decoding of visual attention from LFP signals of macaque MT.

    Directory of Open Access Journals (Sweden)

    Moein Esghaei

    Full Text Available The local field potential (LFP has recently been widely used in brain computer interfaces (BCI. Here we used power of LFP recorded from area MT of a macaque monkey to decode where the animal covertly attended. Support vector machines (SVM were used to learn the pattern of power at different frequencies for attention to two possible positions. We found that LFP power at both low (<9 Hz and high (31-120 Hz frequencies contains sufficient information to decode the focus of attention. Highest decoding performance was found for gamma frequencies (31-120 Hz and reached 82%. In contrast low frequencies (<9 Hz could help the classifier reach a higher decoding performance with a smaller amount of training data. Consequently, we suggest that low frequency LFP can provide fast but coarse information regarding the focus of attention, while higher frequencies of the LFP deliver more accurate but less timely information about the focus of attention.

  9. Impact of Decoding Work within a Professional Program

    Science.gov (United States)

    Yeo, Michelle; Lafave, Mark; Westbrook, Khatija; McAllister, Jenelle; Valdez, Dennis; Eubank, Breda

    2017-01-01

    This chapter demonstrates how Decoding work can be used productively within a curriculum change process to help make design decisions based on a more nuanced understanding of student learning and the relationship of a professional program to the field.

  10. Learning from Decoding across Disciplines and within Communities of Practice

    Science.gov (United States)

    Miller-Young, Janice; Boman, Jennifer

    2017-01-01

    This final chapter synthesizes the findings and implications derived from applying the Decoding the Disciplines model across disciplines and within communities of practice. We make practical suggestions for teachers and researchers who wish to apply and extend this work.

  11. VLSI architecture for a Reed-Solomon decoder

    Science.gov (United States)

    Hsu, In-Shek (Inventor); Truong, Trieu-Kie (Inventor)

    1992-01-01

    A basic single-chip building block for a Reed-Solomon (RS) decoder system is partitioned into a plurality of sections, the first of which consists of a plurality of syndrome subcells each of which contains identical standard-basis finite-field multipliers that are programmable between 10 and 8 bit operation. A desired number of basic building blocks may be assembled to provide a RS decoder of any syndrome subcell size that is programmable between 10 and 8 bit operation.

  12. Interleaved Convolutional Code and Its Viterbi Decoder Architecture

    OpenAIRE

    2003-01-01

    We propose an area-efficient high-speed interleaved Viterbi decoder architecture, which is based on the state-parallel architecture with register exchange path memory structure, for interleaved convolutional code. The state-parallel architecture uses as many add-compare-select (ACS) units as the number of trellis states. By replacing each delay (or storage) element in state metrics memory (or path metrics memory) and path memory (or survival memory) with delays, interleaved Viterbi decoder ...

  13. Evolution of neural computations: Mantis shrimp and human color decoding

    OpenAIRE

    Qasim Zaidi; Justin Marshall; Hanne Thoen; Conway, Bevil R.

    2014-01-01

    Mantis shrimp and primates both possess good color vision, but the neural implementation in the two species is very different, a reflection of the largely unrelated evolutionary lineages of these creatures. Mantis shrimp have scanning compound eyes with 12 classes of photoreceptors, and have evolved a system to decode color information at the front-end of the sensory stream. Primates have image-focusing eyes with three classes of cones, and decode color further along the visual-processing hie...

  14. Performance Analysis of a Decoding Algorithm for Algebraic Geometry Codes

    DEFF Research Database (Denmark)

    Jensen, Helge Elbrønd; Nielsen, Rasmus Refslund; Høholdt, Tom

    1998-01-01

    We analyse the known decoding algorithms for algebraic geometry codes in the case where the number of errors is greater than or equal to [(dFR-1)/2]+1, where dFR is the Feng-Rao distance......We analyse the known decoding algorithms for algebraic geometry codes in the case where the number of errors is greater than or equal to [(dFR-1)/2]+1, where dFR is the Feng-Rao distance...

  15. Decoding Reed-Solomon Codes beyond half the minimum distance

    DEFF Research Database (Denmark)

    Høholdt, Tom; Nielsen, Rasmus Refslund

    1999-01-01

    We describe an efficient implementation of M.Sudan"s algorithm for decoding Reed-Solomon codes beyond half the minimum distance. Furthermore we calculate an upper bound of the probabilty of getting more than one codeword as output......We describe an efficient implementation of M.Sudan"s algorithm for decoding Reed-Solomon codes beyond half the minimum distance. Furthermore we calculate an upper bound of the probabilty of getting more than one codeword as output...

  16. Recent results in the decoding of Algebraic geometry codes

    DEFF Research Database (Denmark)

    Høholdt, Tom; Jensen, Helge Elbrønd; Nielsen, Rasmus Refslund

    1998-01-01

    We analyse the known decoding algorithms for algebraic geometry codes in the case where the number of errors is [(dFR-1)/2]+1, where dFR is the Feng-Rao distance......We analyse the known decoding algorithms for algebraic geometry codes in the case where the number of errors is [(dFR-1)/2]+1, where dFR is the Feng-Rao distance...

  17. Testing interconnected VLSI circuits in the Big Viterbi Decoder

    Science.gov (United States)

    Onyszchuk, I. M.

    1991-01-01

    The Big Viterbi Decoder (BVD) is a powerful error-correcting hardware device for the Deep Space Network (DSN), in support of the Galileo and Comet Rendezvous Asteroid Flyby (CRAF)/Cassini Missions. Recently, a prototype was completed and run successfully at 400,000 or more decoded bits per second. This prototype is a complex digital system whose core arithmetic unit consists of 256 identical very large scale integration (VLSI) gate-array chips, 16 on each of 16 identical boards which are connected through a 28-layer, printed-circuit backplane using 4416 wires. Special techniques were developed for debugging, testing, and locating faults inside individual chips, on boards, and within the entire decoder. The methods are based upon hierarchical structure in the decoder, and require that chips or boards be wired themselves as Viterbi decoders. The basic procedure consists of sending a small set of known, very noisy channel symbols through a decoder, and matching observables against values computed by a software simulation. Also, tests were devised for finding open and short-circuited wires which connect VLSI chips on the boards and through the backplane.

  18. Efficient VLSI architecture of CAVLC decoder with power optimized

    Institute of Scientific and Technical Information of China (English)

    CHEN Guang-hua; HU Deng-ji; ZHANG Jin-yi; ZHENG Wei-feng; ZENG Wei-min

    2009-01-01

    This paper presents an efficient VLSI architecture of the contest-based adaptive variable length code (CAVLC) decoder with power optimized for the H.264/advanced video coding (AVC) standard. In the proposed design, according to the regularity of the codewords, the first one detector is used to solve the low efficiency and high power dissipation problem within the traditional method of table-searching. Considering the relevance of the data used in the process of runbefore's decoding,arithmetic operation is combined with finite state machine (FSM), which achieves higher decoding efficiency. According to the CAVLC decoding flow, clock gating is employed in the module level and the register level respectively, which reduces 43% of the overall dynamic power dissipation. The proposed design can decode every syntax element in one clock cycle. When the proposed design is synthesized at the clock constraint of 100 MHz, the synthesis result shows that the design costs 11 300gates under a 0.25 μm CMOS technology, which meets the demand of real time decoding in the H.264/AVC standard.

  19. Decoding Schemes for FBMC with Single-Delay STTC

    Science.gov (United States)

    Lélé, Chrislin; Le Ruyet, Didier

    2010-12-01

    Orthogonally multiplexed Quadrature Amplitude Modulation (OQAM) with Filter-Bank-based MultiCarrier modulation (FBMC) is a multicarrier modulation scheme that can be considered an alternative to the conventional orthogonal frequency division multiplexing (OFDM) with cyclic prefix (CP) for transmission over multipath fading channels. However, as OQAM-based FBMC is based on real orthogonality, transmission over a complex-valued channel makes the decoding process more challenging compared to CP-OFDM case. Moreover, if we apply Multiple Input Multiple Output (MIMO) techniques to OQAM-based FBMC, the decoding schemes are different from the ones used in CP-OFDM. In this paper, we consider the combination of OQAM-based FBMC with single-delay Space-Time Trellis Coding (STTC). We extend the decoding process presented earlier in the case of [InlineEquation not available: see fulltext.] transmit antennas to greater values of [InlineEquation not available: see fulltext.]. Then, for [InlineEquation not available: see fulltext.], we make an analysis of the theoretical and simulation performance of ML and Viterbi decoding. Finally, to improve the performance of this method, we suggest an iterative decoding method. We show that the OQAM-based FBMC iterative decoding scheme can slightly outperform CP-OFDM.

  20. Decoding Schemes for FBMC with Single-Delay STTC

    Directory of Open Access Journals (Sweden)

    Chrislin Lélé

    2010-01-01

    Full Text Available Orthogonally multiplexed Quadrature Amplitude Modulation (OQAM with Filter-Bank-based MultiCarrier modulation (FBMC is a multicarrier modulation scheme that can be considered an alternative to the conventional orthogonal frequency division multiplexing (OFDM with cyclic prefix (CP for transmission over multipath fading channels. However, as OQAM-based FBMC is based on real orthogonality, transmission over a complex-valued channel makes the decoding process more challenging compared to CP-OFDM case. Moreover, if we apply Multiple Input Multiple Output (MIMO techniques to OQAM-based FBMC, the decoding schemes are different from the ones used in CP-OFDM. In this paper, we consider the combination of OQAM-based FBMC with single-delay Space-Time Trellis Coding (STTC. We extend the decoding process presented earlier in the case of Nt=2 transmit antennas to greater values of Nt. Then, for Nt≥2, we make an analysis of the theoretical and simulation performance of ML and Viterbi decoding. Finally, to improve the performance of this method, we suggest an iterative decoding method. We show that the OQAM-based FBMC iterative decoding scheme can slightly outperform CP-OFDM.

  1. Decoding Schemes for FBMC with Single-Delay STTC

    Directory of Open Access Journals (Sweden)

    Lélé Chrislin

    2010-01-01

    Full Text Available Abstract Orthogonally multiplexed Quadrature Amplitude Modulation (OQAM with Filter-Bank-based MultiCarrier modulation (FBMC is a multicarrier modulation scheme that can be considered an alternative to the conventional orthogonal frequency division multiplexing (OFDM with cyclic prefix (CP for transmission over multipath fading channels. However, as OQAM-based FBMC is based on real orthogonality, transmission over a complex-valued channel makes the decoding process more challenging compared to CP-OFDM case. Moreover, if we apply Multiple Input Multiple Output (MIMO techniques to OQAM-based FBMC, the decoding schemes are different from the ones used in CP-OFDM. In this paper, we consider the combination of OQAM-based FBMC with single-delay Space-Time Trellis Coding (STTC. We extend the decoding process presented earlier in the case of transmit antennas to greater values of . Then, for , we make an analysis of the theoretical and simulation performance of ML and Viterbi decoding. Finally, to improve the performance of this method, we suggest an iterative decoding method. We show that the OQAM-based FBMC iterative decoding scheme can slightly outperform CP-OFDM.

  2. Partially blind instantly decodable network codes for lossy feedback environment

    KAUST Repository

    Sorour, Sameh

    2014-09-01

    In this paper, we study the multicast completion and decoding delay minimization problems for instantly decodable network coding (IDNC) in the case of lossy feedback. When feedback loss events occur, the sender falls into uncertainties about packet reception at the different receivers, which forces it to perform partially blind selections of packet combinations in subsequent transmissions. To determine efficient selection policies that reduce the completion and decoding delays of IDNC in such an environment, we first extend the perfect feedback formulation in our previous works to the lossy feedback environment, by incorporating the uncertainties resulting from unheard feedback events in these formulations. For the completion delay problem, we use this formulation to identify the maximum likelihood state of the network in events of unheard feedback and employ it to design a partially blind graph update extension to the multicast IDNC algorithm in our earlier work. For the decoding delay problem, we derive an expression for the expected decoding delay increment for any arbitrary transmission. This expression is then used to find the optimal policy that reduces the decoding delay in such lossy feedback environment. Results show that our proposed solutions both outperform previously proposed approaches and achieve tolerable degradation even at relatively high feedback loss rates.

  3. Evaluation framework for K-best sphere decoders

    KAUST Repository

    Shen, Chungan

    2010-08-01

    While Maximum-Likelihood (ML) is the optimum decoding scheme for most communication scenarios, practical implementation difficulties limit its use, especially for Multiple Input Multiple Output (MIMO) systems with a large number of transmit or receive antennas. Tree-searching type decoder structures such as Sphere decoder and K-best decoder present an interesting trade-off between complexity and performance. Many algorithmic developments and VLSI implementations have been reported in literature with widely varying performance to area and power metrics. In this semi-tutorial paper we present a holistic view of different Sphere decoding techniques and K-best decoding techniques, identifying the key algorithmic and implementation trade-offs. We establish a consistent benchmark framework to investigate and compare the delay cost, power cost, and power-delay-product cost incurred by each method. Finally, using the framework, we propose and analyze a novel architecture and compare that to other published approaches. Our goal is to explicitly elucidate the overall advantages and disadvantages of each proposed algorithms in one coherent framework. © 2010 World Scientific Publishing Company.

  4. Iterative Decoding of Parallel Concatenated Block Codes and Coset Based MAP Decoding Algorithm for F24 Code

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A multi-dimensional concatenation scheme for block codes is introduced, in which information symbols are interleaved and re-encoded for more than once. It provides a convenient platform to design high performance codes with flexible interleaver size.Coset based MAP soft-in/soft-out decoding algorithms are presented for the F24 code. Simulation results show that the proposed coding scheme can achieve high coding gain with flexible interleaver length and very low decoding complexity.

  5. Singer product apertures-A coded aperture system with a fast decoding algorithm

    Science.gov (United States)

    Byard, Kevin; Shutler, Paul M. E.

    2017-06-01

    A new type of coded aperture configuration that enables fast decoding of the coded aperture shadowgram data is presented. Based on the products of incidence vectors generated from the Singer difference sets, we call these Singer product apertures. For a range of aperture dimensions, we compare experimentally the performance of three decoding methods: standard decoding, induction decoding and direct vector decoding. In all cases the induction and direct vector methods are several orders of magnitude faster than the standard method, with direct vector decoding being significantly faster than induction decoding. For apertures of the same dimensions the increase in speed offered by direct vector decoding over induction decoding is better for lower throughput apertures.

  6. An FPGA Implementation of (3,6-Regular Low-Density Parity-Check Code Decoder

    Directory of Open Access Journals (Sweden)

    Tong Zhang

    2003-05-01

    Full Text Available Because of their excellent error-correcting performance, low-density parity-check (LDPC codes have recently attracted a lot of attention. In this paper, we are interested in the practical LDPC code decoder hardware implementations. The direct fully parallel decoder implementation usually incurs too high hardware complexity for many real applications, thus partly parallel decoder design approaches that can achieve appropriate trade-offs between hardware complexity and decoding throughput are highly desirable. Applying a joint code and decoder design methodology, we develop a high-speed (3,k-regular LDPC code partly parallel decoder architecture based on which we implement a 9216-bit, rate-1/2(3,6-regular LDPC code decoder on Xilinx FPGA device. This partly parallel decoder supports a maximum symbol throughput of 54 Mbps and achieves BER 10−6 at 2 dB over AWGN channel while performing maximum 18 decoding iterations.

  7. Efficient blind decoders for additive spread spectrum embedding based data hiding

    Science.gov (United States)

    Valizadeh, Amir; Wang, Z. Jane

    2012-12-01

    This article investigates efficient blind watermark decoding approaches for hidden messages embedded into host images, within the framework of additive spread spectrum (SS) embedding based for data hiding. We study SS embedding in both the discrete cosine transform and the discrete Fourier transform (DFT) domains. The contributions of this article are multiple-fold: first, we show that the conventional SS scheme could not be applied directly into the magnitudes of the DFT, and thus we present a modified SS scheme and the optimal maximum likelihood (ML) decoder based on the Weibull distribution is derived. Secondly, we investigate the improved spread spectrum (ISS) embedding, an improved technique of the traditional additive SS, and propose the modified ISS scheme for information hiding in the magnitudes of the DFT coefficients and the optimal ML decoders for ISS embedding are derived. We also provide thorough theoretical error probability analysis for the aforementioned decoders. Thirdly, sub-optimal decoders, including local optimum decoder (LOD), generalized maximum likelihood (GML) decoder, and linear minimum mean square error (LMMSE) decoder, are investigated to reduce the required prior information at the receiver side, and their theoretical decoding performances are derived. Based on decoding performances and the required prior information for decoding, we discuss the preferred host domain and the preferred decoder for additive SS-based data hiding under different situations. Extensive simulations are conducted to illustrate the decoding performances of the presented decoders.

  8. Statistical coding and decoding of heartbeat intervals.

    Science.gov (United States)

    Lucena, Fausto; Barros, Allan Kardec; Príncipe, José C; Ohnishi, Noboru

    2011-01-01

    The heart integrates neuroregulatory messages into specific bands of frequency, such that the overall amplitude spectrum of the cardiac output reflects the variations of the autonomic nervous system. This modulatory mechanism seems to be well adjusted to the unpredictability of the cardiac demand, maintaining a proper cardiac regulation. A longstanding theory holds that biological organisms facing an ever-changing environment are likely to evolve adaptive mechanisms to extract essential features in order to adjust their behavior. The key question, however, has been to understand how the neural circuitry self-organizes these feature detectors to select behaviorally relevant information. Previous studies in computational perception suggest that a neural population enhances information that is important for survival by minimizing the statistical redundancy of the stimuli. Herein we investigate whether the cardiac system makes use of a redundancy reduction strategy to regulate the cardiac rhythm. Based on a network of neural filters optimized to code heartbeat intervals, we learn a population code that maximizes the information across the neural ensemble. The emerging population code displays filter tuning proprieties whose characteristics explain diverse aspects of the autonomic cardiac regulation, such as the compromise between fast and slow cardiac responses. We show that the filters yield responses that are quantitatively similar to observed heart rate responses during direct sympathetic or parasympathetic nerve stimulation. Our findings suggest that the heart decodes autonomic stimuli according to information theory principles analogous to how perceptual cues are encoded by sensory systems.

  9. Rate Aware Instantly Decodable Network Codes

    KAUST Repository

    Douik, Ahmed

    2016-02-26

    This paper addresses the problem of reducing the delivery time of data messages to cellular users using instantly decodable network coding (IDNC) with physical-layer rate awareness. While most of the existing literature on IDNC does not consider any physical layer complications, this paper proposes a cross-layer scheme that incorporates the different channel rates of the various users in the decision process of both the transmitted message combinations and the rates with which they are transmitted. The completion time minimization problem in such scenario is first shown to be intractable. The problem is, thus, approximated by reducing, at each transmission, the increase of an anticipated version of the completion time. The paper solves the problem by formulating it as a maximum weight clique problem over a newly designed rate aware IDNC (RA-IDNC) graph. Further, the paper provides a multi-layer solution to improve the completion time approximation. Simulation results suggest that the cross-layer design largely outperforms the uncoded transmissions strategies and the classical IDNC scheme. © 2015 IEEE.

  10. Statistical coding and decoding of heartbeat intervals.

    Directory of Open Access Journals (Sweden)

    Fausto Lucena

    Full Text Available The heart integrates neuroregulatory messages into specific bands of frequency, such that the overall amplitude spectrum of the cardiac output reflects the variations of the autonomic nervous system. This modulatory mechanism seems to be well adjusted to the unpredictability of the cardiac demand, maintaining a proper cardiac regulation. A longstanding theory holds that biological organisms facing an ever-changing environment are likely to evolve adaptive mechanisms to extract essential features in order to adjust their behavior. The key question, however, has been to understand how the neural circuitry self-organizes these feature detectors to select behaviorally relevant information. Previous studies in computational perception suggest that a neural population enhances information that is important for survival by minimizing the statistical redundancy of the stimuli. Herein we investigate whether the cardiac system makes use of a redundancy reduction strategy to regulate the cardiac rhythm. Based on a network of neural filters optimized to code heartbeat intervals, we learn a population code that maximizes the information across the neural ensemble. The emerging population code displays filter tuning proprieties whose characteristics explain diverse aspects of the autonomic cardiac regulation, such as the compromise between fast and slow cardiac responses. We show that the filters yield responses that are quantitatively similar to observed heart rate responses during direct sympathetic or parasympathetic nerve stimulation. Our findings suggest that the heart decodes autonomic stimuli according to information theory principles analogous to how perceptual cues are encoded by sensory systems.

  11. fNIRS-based online deception decoding

    Science.gov (United States)

    Hu, Xiao-Su; Hong, Keum-Shik; Ge, Shuzhi Sam

    2012-04-01

    Deception involves complex neural processes in the brain. Different techniques have been used to study and understand brain mechanisms during deception. Moreover, efforts have been made to develop schemes that can detect and differentiate deception and truth-telling. In this paper, a functional near-infrared spectroscopy (fNIRS)-based online brain deception decoding framework is developed. Deploying dual-wavelength fNIRS, we interrogate 16 locations in the forehead when eight able-bodied adults perform deception and truth-telling scenarios separately. By combining preprocessed oxy-hemoglobin and deoxy-hemoglobin signals, we develop subject-specific classifiers using the support vector machine. Deception and truth-telling states are classified correctly in seven out of eight subjects. A control experiment is also conducted to verify the deception-related hemodynamic response. The average classification accuracy is over 83.44% from these seven subjects. The obtained result suggests that the applicability of fNIRS as a brain imaging technique for online deception detection is very promising.

  12. Decoding reality the universe as quantum information

    CERN Document Server

    Vedral, Vlatko

    2010-01-01

    In Decoding Reality, Vlatko Vedral offers a mind-stretching look at the deepest questions about the universe--where everything comes from, why things are as they are, what everything is. The most fundamental definition of reality is not matter or energy, he writes, but information--and it is the processing of information that lies at the root of all physical, biological, economic, and social phenomena. This view allows Vedral to address a host of seemingly unrelated questions: Why does DNA bind like it does? What is the ideal diet for longevity? How do you make your first million dollars? We can unify all through the understanding that everything consists of bits of information, he writes, though that raises the question of where these bits come from. To find the answer, he takes us on a guided tour through the bizarre realm of quantum physics. At this sub-sub-subatomic level, we find such things as the interaction of separated quantum particles--what Einstein called "spooky action at a distance." In fact, V...

  13. Fast mental states decoding in mixed reality.

    Science.gov (United States)

    De Massari, Daniele; Pacheco, Daniel; Malekshahi, Rahim; Betella, Alberto; Verschure, Paul F M J; Birbaumer, Niels; Caria, Andrea

    2014-01-01

    The combination of Brain-Computer Interface (BCI) technology, allowing online monitoring and decoding of brain activity, with virtual and mixed reality (MR) systems may help to shape and guide implicit and explicit learning using ecological scenarios. Real-time information of ongoing brain states acquired through BCI might be exploited for controlling data presentation in virtual environments. Brain states discrimination during mixed reality experience is thus critical for adapting specific data features to contingent brain activity. In this study we recorded electroencephalographic (EEG) data while participants experienced MR scenarios implemented through the eXperience Induction Machine (XIM). The XIM is a novel framework modeling the integration of a sensing system that evaluates and measures physiological and psychological states with a number of actuators and effectors that coherently reacts to the user's actions. We then assessed continuous EEG-based discrimination of spatial navigation, reading and calculation performed in MR, using linear discriminant analysis (LDA) and support vector machine (SVM) classifiers. Dynamic single trial classification showed high accuracy of LDA and SVM classifiers in detecting multiple brain states as well as in differentiating between high and low mental workload, using a 5 s time-window shifting every 200 ms. Our results indicate overall better performance of LDA with respect to SVM and suggest applicability of our approach in a BCI-controlled MR scenario. Ultimately, successful prediction of brain states might be used to drive adaptation of data representation in order to boost information processing in MR.

  14. Infinity-Norm Sphere-Decoding

    CERN Document Server

    Seethaler, Dominik

    2008-01-01

    The most promising approaches for efficient detection in multiple-input multiple-output (MIMO) wireless systems are based on sphere-decoding (SD). The conventional (and optimum) norm that is used to conduct the tree traversal step in SD is the l-two norm. It was, however, recently shown that using the l-infinity norm instead significantly reduces the VLSI implementation complexity of SD at only a marginal performance loss. These savings are due to a reduction in the length of the critical path and the silicon area of the circuit, but also, as observed previously through simulation results, a consequence of a reduction in the computational (algorithmic) complexity. The aim of this paper is an analytical performance and computational complexity analysis of l-infinity norm SD. For i.i.d. Rayleigh fading MIMO channels, we show that l-infinity norm SD achieves full diversity order with an asymptotic SNR gap, compared to l-two norm SD, that increases at most linearly in the number of receive antennas. Moreover, we ...

  15. Cognitive Wyner Networks with Clustered Decoding

    CERN Document Server

    Lapidoth, Amos; Shamai, Shlomo; Wigger, Michele

    2012-01-01

    We study the uplink of linear cellular models featuring short range inter-cell interference. This means, we study $K$-transmitter/$K$-receiver interference networks where the transmitters lie on a line and the receivers on a parallel line; each receiver opposite its corresponding transmitter. We assume short-range interference by which we mean that the signal sent by a given transmitter is only interfered either by the signal sent by its left neighbor (we refer to this setup as the asymmetric network) or by the signals sent by both its neighbors (we refer to this setup as the symmetric network). We assume that each transmitter has side-information consisting of the messages of the $t_\\ell$ transmitters to its left and the $t_r$ transmitters to its right, and that each receiver can decode its message using the signals received at its own antenna, at the $r_\\ell$ receiving antennas to its left, and at the $r_r$ receiving antennas to its right. We provide upper and lower bounds on the multiplexing gain of these ...

  16. Why Hawking Radiation Cannot Be Decoded

    CERN Document Server

    Ong, Yen Chin; Chen, Pisin

    2014-01-01

    One of the great difficulties in the theory of black hole evaporation is that the most decisive phenomena tend to occur when the black hole is extremely hot: that is, when the physics is most poorly understood. Fortunately, a crucial step in the Harlow-Hayden approach to the firewall paradox, concerning the time available for decoding of Hawking radiation emanating from charged AdS black holes, can be made to work without relying on the unknown physics of black holes with extremely high temperatures; in fact, it relies on the properties of cold black holes. Here we clarify this surprising point. The approach is based on ideas borrowed from applications of the AdS/CFT correspondence to the quark-gluon plasma. Firewalls aside, our work presents a detailed analysis of the thermodynamics and evolution of evaporating charged AdS black holes with flat event horizons. We show that, in one way or another, these black holes are always eventually destroyed in a time which, while long by normal standards, is short relat...

  17. Fast mental states decoding in mixed reality.

    Directory of Open Access Journals (Sweden)

    Daniele eDe Massari

    2014-11-01

    Full Text Available The combination of Brain-Computer Interface technology, allowing online monitoring and decoding of brain activity, with virtual and mixed reality systems may help to shape and guide implicit and explicit learning using ecological scenarios. Real-time information of ongoing brain states acquired through BCI might be exploited for controlling data presentation in virtual environments. In this context, assessing to what extent brain states can be discriminated during mixed reality experience is critical for adapting specific data features to contingent brain activity. In this study we recorded EEG data while participants experienced a mixed reality scenario implemented through the eXperience Induction Machine (XIM. The XIM is a novel framework modeling the integration of a sensing system that evaluates and measures physiological and psychological states with a number of actuators and effectors that coherently reacts to the user's actions. We then assessed continuous EEG-based discrimination of spatial navigation, reading and calculation performed in mixed reality, using LDA and SVM classifiers. Dynamic single trial classification showed high accuracy of LDA and SVM classifiers in detecting multiple brain states as well as in differentiating between high and low mental workload, using a 5 s time-window shifting every 200 ms. Our results indicate overall better performance of LDA with respect to SVM and suggest applicability of our approach in a BCI-controlled mixed reality scenario. Ultimately, successful prediction of brain states might be used to drive adaptation of data representation in order to boost information processing in mixed reality.

  18. PERFORMANCE OF A NEW DECODING METHOD USED IN OPEN-LOOP ALL-OPTICAL CHAOTIC COMMUNICATION SYSTEM

    Institute of Scientific and Technical Information of China (English)

    Liu Huijie; Feng Jiuchao

    2011-01-01

    A new decoding method with decoder is used in open-loop all-optical chaotic communication system under strong injection condition.The performance of the new decoding method is numerically investigated by comparing it with the common decoding method without decoder.For new decoding method,two cases are analyzed,including whether or not the output of the decoder is adjusted by its input to receiver.The results indicate the decoding quality can be improved by adjusting for the new decoding method.Meanwhile,the injection strength of decoder can be restricted in a certain range.The adjusted new decoding method with decoder can achieve better decoding quality than decoding method without decoder when the bit rate of message is under 5 Gb/s.However,a stronger injection for receiver is needed.Moreover,the new decoding method can broaden the range of injection strength acceptable for good decoding quality.Different message encryption techniques are tested,and the result is similar to that of the common decoding method,indicative of the fact that the message encoded by using Chaotic Modulation (CM) can be best recovered by the new decoding method owning to the essence of this encryption technique.

  19. A real-time MPEG software decoder using a portable message-passing library

    Energy Technology Data Exchange (ETDEWEB)

    Kwong, Man Kam; Tang, P.T. Peter; Lin, Biquan

    1995-12-31

    We present a real-time MPEG software decoder that uses message-passing libraries such as MPL, p4 and MPI. The parallel MPEG decoder currently runs on the IBM SP system but can be easil ported to other parallel machines. This paper discusses our parallel MPEG decoding algorithm as well as the parallel programming environment under which it uses. Several technical issues are discussed, including balancing of decoding speed, memory limitation, 1/0 capacities, and optimization of MPEG decoding components. This project shows that a real-time portable software MPEG decoder is feasible in a general-purpose parallel machine.

  20. Reconfigurable and Parallelized Network Coding Decoder for VANETs

    Directory of Open Access Journals (Sweden)

    Sunwoo Kim

    2012-01-01

    Full Text Available Network coding is a promising technique for data communications in wired and wireless networks. However, it places an additional computing overhead on the receiving node in exchange for the improved bandwidth. This paper proposes an FPGA-based reconfigurable and parallelized network coding decoder for embedded systems especially for vehicular ad hoc networks. In our design, rapid decoding process can be achieved by exploiting parallelism in the coefficient vector operations. The proposed decoder is implemented by using a modern Xilinx Virtex-5 device and its performance is evaluated considering the performance of the software decoding on various embedded processors. The performance on four different sizes of the coefficient matrix is measured and the decoding throughput of 18.3 Mbps for the size 16 × 16 and 6.5 Mbps for 128 × 128 has been achieved at the operating frequency of 64.5 MHz. Compared to the recent TEGRA 250 processor, the result obtained with128 × 128 coefficient matrix reaches up to 5.06 in terms of speedup.

  1. Distributed coding/decoding complexity in video sensor networks.

    Science.gov (United States)

    Cordeiro, Paulo J; Assunção, Pedro

    2012-01-01

    Video Sensor Networks (VSNs) are recent communication infrastructures used to capture and transmit dense visual information from an application context. In such large scale environments which include video coding, transmission and display/storage, there are several open problems to overcome in practical implementations. This paper addresses the most relevant challenges posed by VSNs, namely stringent bandwidth usage and processing time/power constraints. In particular, the paper proposes a novel VSN architecture where large sets of visual sensors with embedded processors are used for compression and transmission of coded streams to gateways, which in turn transrate the incoming streams and adapt them to the variable complexity requirements of both the sensor encoders and end-user decoder terminals. Such gateways provide real-time transcoding functionalities for bandwidth adaptation and coding/decoding complexity distribution by transferring the most complex video encoding/decoding tasks to the transcoding gateway at the expense of a limited increase in bit rate. Then, a method to reduce the decoding complexity, suitable for system-on-chip implementation, is proposed to operate at the transcoding gateway whenever decoders with constrained resources are targeted. The results show that the proposed method achieves good performance and its inclusion into the VSN infrastructure provides an additional level of complexity control functionality.

  2. Combinatorial limitations of a strong form of list decoding

    CERN Document Server

    Guruswami, Venkatesan

    2012-01-01

    We prove the following results concerning the combinatorics of list decoding, motivated by the exponential gap between the known upper bound (of $O(1/\\gamma)$) and lower bound (of $\\Omega_p(\\log (1/\\gamma))$) for the list-size needed to decode up to radius $p$ with rate $\\gamma$ away from capacity, i.e., $1-\\h(p)-\\gamma$ (here $p\\in (0,1/2)$ and $\\gamma > 0$). We prove that in any binary code $C \\subseteq \\{0,1\\}^n$ of rate $1-\\h(p)-\\gamma$, there must exist a set $\\mathcal{L} \\subset C$ of $\\Omega_p(1/\\sqrt{\\gamma})$ codewords such that the average distance of the points in $\\mathcal{L}$ from their centroid is at most $pn$. In other words, there must exist $\\Omega_p(1/\\sqrt{\\gamma})$ codewords with low "average radius". The motivation for this result is that it gives a list-size lower bound for a strong notion of list decoding which has been implicitly been used in the previous negative results for list decoding. (The usual notion of list decoding corresponds to replacing {\\em average} radius by the {\\em min...

  3. Robust pattern decoding in shape-coded structured light

    Science.gov (United States)

    Tang, Suming; Zhang, Xu; Song, Zhan; Song, Lifang; Zeng, Hai

    2017-09-01

    Decoding is a challenging and complex problem in a coded structured light system. In this paper, a robust pattern decoding method is proposed for the shape-coded structured light in which the pattern is designed as grid shape with embedded geometrical shapes. In our decoding method, advancements are made at three steps. First, a multi-template feature detection algorithm is introduced to detect the feature point which is the intersection of each two orthogonal grid-lines. Second, pattern element identification is modelled as a supervised classification problem and the deep neural network technique is applied for the accurate classification of pattern elements. Before that, a training dataset is established, which contains a mass of pattern elements with various blurring and distortions. Third, an error correction mechanism based on epipolar constraint, coplanarity constraint and topological constraint is presented to reduce the false matches. In the experiments, several complex objects including human hand are chosen to test the accuracy and robustness of the proposed method. The experimental results show that our decoding method not only has high decoding accuracy, but also owns strong robustness to surface color and complex textures.

  4. Performance evaluation of H.264 decoder on different processors

    Directory of Open Access Journals (Sweden)

    H.S.Prasantha

    2010-08-01

    Full Text Available H.264/AVC (Advanced Video Coding is the newest video coding standard of the moving video coding experts group. The decoder is standardized by imposing restrictions on the bit stream and syntax, and defining the process of decoding syntax elements such that every decoder conforming to the standard will produce similar output when encoded bit stream is provided as input. It uses state of art coding tools and provides enhanced coding efficiency for a wide range of applications, including video telephony, real-time video conferencing, direct-broadcast TV (television, blue-ray disc, DVB (Digital video broadcast broadcast, streaming video and others. The paper proposes to port the H.264/AVC decoder on the various processors such as TI DSP (Digital signal processor, ARM (Advanced risk machines and P4 (Pentium processors. The paper also proposesto analyze and compare Video Quality Metrics for different encoded video sequences. The paper proposes to investigate the decoder performance on different processors with and without deblocking filter and compare the performance based on different video quality measures.

  5. Measuring Integrated Information from the Decoding Perspective.

    Directory of Open Access Journals (Sweden)

    Masafumi Oizumi

    2016-01-01

    Full Text Available Accumulating evidence indicates that the capacity to integrate information in the brain is a prerequisite for consciousness. Integrated Information Theory (IIT of consciousness provides a mathematical approach to quantifying the information integrated in a system, called integrated information, Φ. Integrated information is defined theoretically as the amount of information a system generates as a whole, above and beyond the amount of information its parts independently generate. IIT predicts that the amount of integrated information in the brain should reflect levels of consciousness. Empirical evaluation of this theory requires computing integrated information from neural data acquired from experiments, although difficulties with using the original measure Φ precludes such computations. Although some practical measures have been previously proposed, we found that these measures fail to satisfy the theoretical requirements as a measure of integrated information. Measures of integrated information should satisfy the lower and upper bounds as follows: The lower bound of integrated information should be 0 and is equal to 0 when the system does not generate information (no information or when the system comprises independent parts (no integration. The upper bound of integrated information is the amount of information generated by the whole system. Here we derive the novel practical measure Φ* by introducing a concept of mismatched decoding developed from information theory. We show that Φ* is properly bounded from below and above, as required, as a measure of integrated information. We derive the analytical expression of Φ* under the Gaussian assumption, which makes it readily applicable to experimental data. Our novel measure Φ* can generally be used as a measure of integrated information in research on consciousness, and also as a tool for network analysis on diverse areas of biology.

  6. Measuring Integrated Information from the Decoding Perspective.

    Science.gov (United States)

    Oizumi, Masafumi; Amari, Shun-ichi; Yanagawa, Toru; Fujii, Naotaka; Tsuchiya, Naotsugu

    2016-01-01

    Accumulating evidence indicates that the capacity to integrate information in the brain is a prerequisite for consciousness. Integrated Information Theory (IIT) of consciousness provides a mathematical approach to quantifying the information integrated in a system, called integrated information, Φ. Integrated information is defined theoretically as the amount of information a system generates as a whole, above and beyond the amount of information its parts independently generate. IIT predicts that the amount of integrated information in the brain should reflect levels of consciousness. Empirical evaluation of this theory requires computing integrated information from neural data acquired from experiments, although difficulties with using the original measure Φ precludes such computations. Although some practical measures have been previously proposed, we found that these measures fail to satisfy the theoretical requirements as a measure of integrated information. Measures of integrated information should satisfy the lower and upper bounds as follows: The lower bound of integrated information should be 0 and is equal to 0 when the system does not generate information (no information) or when the system comprises independent parts (no integration). The upper bound of integrated information is the amount of information generated by the whole system. Here we derive the novel practical measure Φ* by introducing a concept of mismatched decoding developed from information theory. We show that Φ* is properly bounded from below and above, as required, as a measure of integrated information. We derive the analytical expression of Φ* under the Gaussian assumption, which makes it readily applicable to experimental data. Our novel measure Φ* can generally be used as a measure of integrated information in research on consciousness, and also as a tool for network analysis on diverse areas of biology.

  7. On the Optimality of Successive Decoding in Compress-and-Forward Relay Schemes

    CERN Document Server

    Wu, Xiugang

    2010-01-01

    In the classical compress-and-forward relay scheme developed by (Cover and El Gamal, 1979), the decoding process operates in a successive way: the destination first decodes the compressed observation of the relay, and then decodes the original message of the source. Recently, two modified compress-and-forward relay schemes were proposed, and in both of them, the destination jointly decodes the compressed observation of the relay and the original message, instead of successively. Such a modification on the decoding process was motivated by realizing that it is generally easier to decode the compressed observation jointly with the original message, and more importantly, the original message can be decoded even without completely decoding the compressed observation. However, the question remains whether this freedom of choosing a higher compression rate at the relay improves the achievable rate of the original message. It has been shown in (El Gamal and Kim, 2010) that the answer is negative in the single relay ...

  8. A General Rate K/N Convolutional Decoder Based on Neural Networks with Stopping Criterion

    Directory of Open Access Journals (Sweden)

    Johnny W. H. Kao

    2009-01-01

    Full Text Available A novel algorithm for decoding a general rate K/N convolutional code based on recurrent neural network (RNN is described and analysed. The algorithm is introduced by outlining the mathematical models of the encoder and decoder. A number of strategies for optimising the iterative decoding process are proposed, and a simulator was also designed in order to compare the Bit Error Rate (BER performance of the RNN decoder with the conventional decoder that is based on Viterbi Algorithm (VA. The simulation results show that this novel algorithm can achieve the same bit error rate and has a lower decoding complexity. Most importantly this algorithm allows parallel signal processing, which increases the decoding speed and accommodates higher data rate transmission. These characteristics are inherited from a neural network structure of the decoder and the iterative nature of the algorithm, that outperform the conventional VA algorithm.

  9. Map Algorithms for Decoding Linear Block codes Based on Sectionalized Trellis Diagrams

    Science.gov (United States)

    Lin, Shu

    1999-01-01

    The MAP algorithm is a trellis-based maximum a posteriori probability decoding algorithm. It is the heart of the turbo (or iterative) decoding which achieves an error performance near the Shannon limit. Unfortunately, the implementation of this algorithm requires large computation and storage. Furthermore, its forward and backward recursions result in long decoding delay. For practical applications, this decoding algorithm must be simplified and its decoding complexity and delay must be reduced. In this paper, the MAP algorithm and its variations, such as Log-MAP and Max-Log-MAP algorithms, are first applied to sectionalized trellises for linear block codes and carried out as two-stage decodings. Using the structural properties of properly sectionalized trellises, the decoding complexity and delay of the MAP algorithms can be reduced. Computation-wise optimum sectionalizations of a trellis for MAP algorithms are investigated. Also presented in this paper are bi-directional and parallel MAP decodings.

  10. A Concatenated ML Decoder for ST/SFBC-OFDM Systems in Double Selective Fading Channels

    Institute of Scientific and Technical Information of China (English)

    李明齐; 张文军

    2004-01-01

    This paper presented a concatenated maximum-likelihood (ML) decoder for space-time/space-frequency block coded orthogonal frequency diversion multiplexing (ST/SFBC-OFDM) systems in double selective fading channels. The proposed decoder first detects space-time or space-frequency codeword elements separately. Then, according to the coarsely estimated codeword elements, the ML decoding is performed in a smaller constellation element set to searching final codeword. It is proved that the proposed decoder has optimal performances if and only if subchannels are constant during a codeword interval. The simulation results show that the performances of proposed decoder is close to that of the optimal ML decoder in severe Doppler and delay spread channels. However, the complexity of proposed decoder is much lower than that of the optimal ML decoder.

  11. A Discrete Time Markov Chain Model for High Throughput Bidirectional Fano Decoders

    CERN Document Server

    Xu, Ran; Morris, Kevin; Kocak, Taskin

    2010-01-01

    The bidirectional Fano algorithm (BFA) can achieve at least two times decoding throughput compared to the conventional unidirectional Fano algorithm (UFA). In this paper, bidirectional Fano decoding is examined from the queuing theory perspective. A Discrete Time Markov Chain (DTMC) is employed to model the BFA decoder with a finite input buffer. The relationship between the input data rate, the input buffer size and the clock speed of the BFA decoder is established. The DTMC based modelling can be used in designing a high throughput parallel BFA decoding system. It is shown that there is a tradeoff between the number of BFA decoders and the input buffer size, and an optimal input buffer size can be chosen to minimize the hardware complexity for a target decoding throughput in designing a high throughput parallel BFA decoding system.

  12. Multistep Linear Programming Approaches for Decoding Low-Density Parity-Check Codes

    Institute of Scientific and Technical Information of China (English)

    LIU Haiyang; MA Lianrong; CHEN Jie

    2009-01-01

    The problem of improving the performance of linear programming (LP) decoding of low-density padty-check (LDPC) codes is considered in this paper. A multistep linear programming (MLP) algorithm was developed for decoding LDPC codes that includes a slight increase in computational complexity. The MLP decoder adaptively adds new constraints which are compatible with a selected check node to refine the re-sults when an error is reported by the odginal LP decoder. The MLP decoder result is shown to have the maximum-likelihood (ML) certificate property. Simulations with moderate block length LDPC codes suggest that the MLP decoder gives better performance than both the odginal LP decoder and the conventional sum-product (SP) decoder.

  13. A Low Power Viterbi Decoder for Trellis Coded Modulation System

    Directory of Open Access Journals (Sweden)

    M. Jansi Rani

    2014-02-01

    Full Text Available Forward Error Correction (FEC schemes are an essential component of wireless communication systems. Convolutional codes are employed to implement FEC but the complexity of corresponding decoders increases exponentially according to the constraint length. Present wireless standards such as Third generation (3G systems, GSM, 802.11A, 802.16 utilize some configuration of convolutional coding. Convolutional encoding with Viterbi decoding is a powerful method for forward error correction. Viterbi algorithm is the most extensively employed decoding algorithm for convolutional codes. The main aim of this project is to design FPGA based Viterbi algorithm which encrypts / decrypts the data. In this project the encryption / decryption algorithm is designed and programmed in to the FPGA.

  14. Analysis of Minimal LDPC Decoder System on a Chip Implementation

    Directory of Open Access Journals (Sweden)

    T. Palenik

    2015-09-01

    Full Text Available This paper presents a practical method of potential replacement of several different Quasi-Cyclic Low-Density Parity-Check (QC-LDPC codes with one, with the intention of saving as much memory as required to implement the LDPC encoder and decoder in a memory-constrained System on a Chip (SoC. The presented method requires only a very small modification of the existing encoder and decoder, making it suitable for utilization in a Software Defined Radio (SDR platform. Besides the analysis of the effects of necessary variable-node value fixation during the Belief Propagation (BP decoding algorithm, practical standard-defined code parameters are scrutinized in order to evaluate the feasibility of the proposed LDPC setup simplification. Finally, the error performance of the modified system structure is evaluated and compared with the original system structure by means of simulation.

  15. Novel Quaternary Quantum Decoder, Multiplexer and Demultiplexer Circuits

    Science.gov (United States)

    Haghparast, Majid; Monfared, Asma Taheri

    2017-05-01

    Multiple valued logic is a promising approach to reduce the width of the reversible or quantum circuits, moreover, quaternary logic is considered as being a good choice for future quantum computing technology hence it is very suitable for the encoded realization of binary logic functions through its grouping of 2-bits together into quaternary values. The Quaternary decoder, multiplexer, and demultiplexer are essential units of quaternary digital systems. In this paper, we have initially designed a quantum realization of the quaternary decoder circuit using quaternary 1-qudit gates and quaternary Muthukrishnan-Stroud gates. Then we have presented quantum realization of quaternary multiplexer and demultiplexer circuits using the constructed quaternary decoder circuit and quaternary controlled Feynman gates. The suggested circuits in this paper have a lower quantum cost and hardware complexity than the existing designs that are currently used in quaternary digital systems. All the scales applied in this paper are based on Nanometric area.

  16. Novel Quaternary Quantum Decoder, Multiplexer and Demultiplexer Circuits

    Science.gov (United States)

    Haghparast, Majid; Monfared, Asma Taheri

    2017-02-01

    Multiple valued logic is a promising approach to reduce the width of the reversible or quantum circuits, moreover, quaternary logic is considered as being a good choice for future quantum computing technology hence it is very suitable for the encoded realization of binary logic functions through its grouping of 2-bits together into quaternary values. The Quaternary decoder, multiplexer, and demultiplexer are essential units of quaternary digital systems. In this paper, we have initially designed a quantum realization of the quaternary decoder circuit using quaternary 1-qudit gates and quaternary Muthukrishnan-Stroud gates. Then we have presented quantum realization of quaternary multiplexer and demultiplexer circuits using the constructed quaternary decoder circuit and quaternary controlled Feynman gates. The suggested circuits in this paper have a lower quantum cost and hardware complexity than the existing designs that are currently used in quaternary digital systems. All the scales applied in this paper are based on Nanometric area.

  17. SERS decoding of micro gold shells moving in microfluidic systems.

    Science.gov (United States)

    Lee, Saram; Joo, Segyeong; Park, Sejin; Kim, Soyoun; Kim, Hee Chan; Chung, Taek Dong

    2010-05-01

    In this study, in situ surface-enhanced Raman scattering (SERS) decoding was demonstrated in microfluidic chips using novel thin micro gold shells modified with Raman tags. The micro gold shells were fabricated using electroless gold plating on PMMA beads with diameter of 15 microm. These shells were sophisticatedly optimized to produce the maximum SERS intensity, which minimized the exposure time for quick and safe decoding. The shell surfaces produced well-defined SERS spectra even at an extremely short exposure time, 1 ms, for a single micro gold shell combined with Raman tags such as 2-naphthalenethiol and benzenethiol. The consecutive SERS spectra from a variety of combinations of Raman tags were successfully acquired from the micro gold shells moving in 25 microm deep and 75 microm wide channels on a glass microfluidic chip. The proposed functionalized micro gold shells exhibited the potential of an on-chip microfluidic SERS decoding strategy for micro suspension array.

  18. HIGH THROUGHPUT OF MAP PROCESSOR USING PIPELINE WINDOW DECODING

    Directory of Open Access Journals (Sweden)

    P. Nithya

    2012-11-01

    Full Text Available Turbo codes are one of the most efficient error correcting code which approaches the Shannon limit.The high throughput in turbo decoder can be achieved by parallelizing several soft Input Soft Output(SISOunits together.In this way,multiple SISO decoders work on the same data frame at the same values and delievers soft outputs can be split into three terms like the soft channel and a priori input and the extrinsic value.The extrinsic value is used for the next iteration.The high throughput of Max-Log-MAP processor tha supports both single Binary(SBand Double-binary(DB convolutional turbo codes.Decoding of these codes however an iterative processing is requires high computation rate and latency.Thus in order to achieve high throughput and to reduce latency by using serial processing techniques.The pipeline window(PWdecoding is introduced to support arbitrary frame sizes with high throughput.

  19. Modified Suboptimal Iterative Decoding for Regular Repeat- Accumulate Coded Signals

    Directory of Open Access Journals (Sweden)

    Muhammad Thamer Nesr

    2017-05-01

    Full Text Available In this work, two algorithms are suggested in order to improve the performance of systematic Repeat-Accumulate ( decoding. The first one is accomplished by the insertion of pilot symbols among the data stream that entering the encoder. The positions where pilots should be inserted are chosen in such a way that to improve the minimum Hamming distance and/or to reduce the error coefficients of the code. The second proposed algorithm includes the utilization of the inserted pilots to estimate scaling (correction factors. Two-dimensional correction factor was suggested in order to enhance the performance of traditional Minimum-Sum decoding of regular repeat accumulate codes. An adaptive method can be achieved for getting the correction factors by calculating the mean square difference between the values of received pilots and the a-posteriori data of bit and check node related to them which created by the minimum-sum ( decoder

  20. Joint scheduling and resource allocation for multiple video decoding tasks

    Science.gov (United States)

    Foo, Brian; van der Schaar, Mihaela

    2008-01-01

    In this paper we propose a joint resource allocation and scheduling algorithm for video decoding on a resource-constrained system. By decomposing a multimedia task into decoding jobs using quality-driven priority classes, we demonstrate using queuing theoretic analysis that significant power savings can be achieved under small video quality degradation without requiring the encoder to adapt its transmitted bitstream. Based on this scheduling algorithm, we propose an algorithm for maximizing the sum of video qualities in a multiple task environment, while minimizing system energy consumption, without requiring tasks to reveal information about their performances to the system or to other potentially exploitative applications. Importantly, we offer a method to optimize the performance of multiple video decoding tasks on an energy-constrained system, while protecting private information about the system and the applications.

  1. Ternary Tree and Memory-Efficient Huffman Decoding Algorithm

    Directory of Open Access Journals (Sweden)

    Pushpa R. Suri

    2011-01-01

    Full Text Available In this study, the focus was on the use of ternary tree over binary tree. Here, a new one pass Algorithm for Decoding adaptive Huffman ternary tree codes was implemented. To reduce the memory size and fasten the process of searching for a symbol in a Huffman tree, we exploited the property of the encoded symbols and proposed a memory efficient data structure to represent the codeword length of Huffman ternary tree. In this algorithm we tried to find out the staring and ending address of the code to know the length of the code. And then in second algorithm we tried to decode the ternary tree code using binary search method. In this algorithm we tried to find out the staring and ending address of the code to know the length of the code. And then in second algorithm we tried to decode the ternary tree code using binary search method.

  2. 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...

  3. Sparsity-Aware Sphere Decoding: Algorithms and Complexity Analysis

    Science.gov (United States)

    Barik, Somsubhra; Vikalo, Haris

    2014-05-01

    Integer least-squares problems, concerned with solving a system of equations where the components of the unknown vector are integer-valued, arise in a wide range of applications. In many scenarios the unknown vector is sparse, i.e., a large fraction of its entries are zero. Examples include applications in wireless communications, digital fingerprinting, and array-comparative genomic hybridization systems. Sphere decoding, commonly used for solving integer least-squares problems, can utilize the knowledge about sparsity of the unknown vector to perform computationally efficient search for the solution. In this paper, we formulate and analyze the sparsity-aware sphere decoding algorithm that imposes $\\ell_0$-norm constraint on the admissible solution. Analytical expressions for the expected complexity of the algorithm for alphabets typical of sparse channel estimation and source allocation applications are derived and validated through extensive simulations. The results demonstrate superior performance and speed of sparsity-aware sphere decoder compared to the conventional sparsity-unaware sphere decoding algorithm. Moreover, variance of the complexity of the sparsity-aware sphere decoding algorithm for binary alphabets is derived. The search space of the proposed algorithm can be further reduced by imposing lower bounds on the value of the objective function. The algorithm is modified to allow for such a lower bounding technique and simulations illustrating efficacy of the method are presented. Performance of the algorithm is demonstrated in an application to sparse channel estimation, where it is shown that sparsity-aware sphere decoder performs close to theoretical lower limits.

  4. Polytope Representations for Linear-Programming Decoding of Non-Binary Linear Codes

    CERN Document Server

    Skachek, Vitaly; Byrne, Eimear; Greferath, Marcus

    2007-01-01

    In previous work, we demonstrated how decoding of a non-binary linear code could be formulated as a linear-programming problem. In this paper, we study different polytopes for use with linear-programming decoding, and show that for many classes of codes these polytopes yield a complexity advantage for decoding. These representations lead to polynomial-time decoders for a wide variety of classical non-binary linear codes.

  5. Algebraic Fast-Decodable Relay Codes for Distributed Communications

    CERN Document Server

    Hollanti, Camilla

    2012-01-01

    In this paper, fast-decodable lattice code constructions are designed for the nonorthogonal amplify-and-forward (NAF) multiple-input multiple-output (MIMO) channel. The constructions are based on different types of algebraic structures, e.g. quaternion division algebras. When satisfying certain properties, these algebras provide us with codes whose structure naturally reduces the decoding complexity. The complexity can be further reduced by shortening the block length, i.e., by considering rectangular codes called less than minimum delay (LMD) codes.

  6. New Iterated Decoding Algorithm Based on Differential Frequency Hopping System

    Institute of Scientific and Technical Information of China (English)

    LIANG Fu-lin; LUO Wei-xiong

    2005-01-01

    A new iterated decoding algorithm is proposed for differential frequency hopping (DFH) encoder concatenated with multi-frequency shift-key (MFSK) modulator. According to the character of the frequency hopping (FH) pattern trellis produced by DFH function, maximum a posteriori (MAP) probability theory is applied to realize the iterate decoding of it. Further, the initial conditions for the new iterate algorithm based on MAP algorithm are modified for better performance. Finally, the simulation result compared with that from traditional algorithms shows good anti-interference performance.

  7. Joint Estimation and Decoding of Space-Time Trellis Codes

    Directory of Open Access Journals (Sweden)

    Zhang Jianqiu

    2002-01-01

    Full Text Available We explore the possibility of using an emerging tool in statistical signal processing, sequential importance sampling (SIS, for joint estimation and decoding of space-time trellis codes (STTC. First, we provide background on SIS, and then we discuss its application to space-time trellis code (STTC systems. It is shown through simulations that SIS is suitable for joint estimation and decoding of STTC with time-varying flat-fading channels when phase ambiguity is avoided. We used a design criterion for STTCs and temporally correlated channels that combats phase ambiguity without pilot signaling. We have shown by simulations that the design is valid.

  8. Decoding Brain States Based on Magnetoencephalography From Prespecified Cortical Regions.

    Science.gov (United States)

    Zhang, Jinyin; Li, Xin; Foldes, Stephen T; Wang, Wei; Collinger, Jennifer L; Weber, Douglas J; Bagić, Anto

    2016-01-01

    Brain state decoding based on whole-head MEG has been extensively studied over the past decade. Recent MEG applications pose an emerging need of decoding brain states based on MEG signals originating from prespecified cortical regions. Toward this goal, we propose a novel region-of-interest-constrained discriminant analysis algorithm (RDA) in this paper. RDA integrates linear classification and beamspace transformation into a unified framework by formulating a constrained optimization problem. Our experimental results based on human subjects demonstrate that RDA can efficiently extract the discriminant pattern from prespecified cortical regions to accurately distinguish different brain states.

  9. EXIT Chart Analysis of Binary Message-Passing Decoders

    DEFF Research Database (Denmark)

    Lechner, Gottfried; Pedersen, Troels; Kramer, Gerhard

    2007-01-01

    Binary message-passing decoders for LDPC codes are analyzed using EXIT charts. For the analysis, the variable node decoder performs all computations in the L-value domain. For the special case of a hard decision channel, this leads to the well know Gallager B algorithm, while the analysis can...... be extended to channels with larger output alphabets. By increasing the output alphabet from hard decisions to four symbols, a gain of more than 1.0 dB is achieved using optimized codes. For this code optimization, the mixing property of EXIT functions has to be modified to the case of binary message-passing...

  10. Adaptive neuron-to-EMG decoder training for FES neuroprostheses

    Science.gov (United States)

    Ethier, Christian; Acuna, Daniel; Solla, Sara A.; Miller, Lee E.

    2016-08-01

    Objective. We have previously demonstrated a brain-machine interface neuroprosthetic system that provided continuous control of functional electrical stimulation (FES) and restoration of grasp in a primate model of spinal cord injury (SCI). Predicting intended EMG directly from cortical recordings provides a flexible high-dimensional control signal for FES. However, no peripheral signal such as force or EMG is available for training EMG decoders in paralyzed individuals. Approach. Here we present a method for training an EMG decoder in the absence of muscle activity recordings; the decoder relies on mapping behaviorally relevant cortical activity to the inferred EMG activity underlying an intended action. Monkeys were trained at a 2D isometric wrist force task to control a computer cursor by applying force in the flexion, extension, ulnar, and radial directions and execute a center-out task. We used a generic muscle force-to-endpoint force model based on muscle pulling directions to relate each target force to an optimal EMG pattern that attained the target force while minimizing overall muscle activity. We trained EMG decoders during the target hold periods using a gradient descent algorithm that compared EMG predictions to optimal EMG patterns. Main results. We tested this method both offline and online. We quantified both the accuracy of offline force predictions and the ability of a monkey to use these real-time force predictions for closed-loop cursor control. We compared both offline and online results to those obtained with several other direct force decoders, including an optimal decoder computed from concurrently measured neural and force signals. Significance. This novel approach to training an adaptive EMG decoder could make a brain-control FES neuroprosthesis an effective tool to restore the hand function of paralyzed individuals. Clinical implementation would make use of individualized EMG-to-force models. Broad generalization could be achieved by

  11. Conventional Tanner Graph for Recursive onvolutional Codes and Associated Decoding

    Institute of Scientific and Technical Information of China (English)

    SUN Hong

    2001-01-01

    A different representation of recur-sive systematic convolutional (RSC) codes is pro-posed. This representation can be realized by a con-ventional Tanner graph. The graph becomes a treeby introducing hidden edge. It is shown that thesum-product algorithm applied to this graph modelis equivalent to the BCJR algorithm for turbo de-coding with lower computational complexity. Themessage-passing chain of the BCJR algorithm is pre-sented more exactly in the graph. In addition, theproposed representation of RSC codes provides an ef-ficient method to set up the trellis and the conven-tional Tanner graph for RSC codes provides directlythe architecture for decoding.

  12. Optimal encoding and decoding of a spin direction

    CERN Document Server

    Bagán, E; Brey, A; Muñoz-Tàpia, R; Tarrach, Rolf

    2001-01-01

    For a system of N spins 1/2 there are quantum states that can encode a direction in an intrinsic way. Information on this direction can later be decoded by means of a quantum measurement. We present here the optimal encoding and decoding procedure using the fidelity as a figure of merit. We compute the maximal fidelity and prove that it is directly related to the largest zeroes of the Legendre and Jacobi polynomials. We show that this maximal fidelity approaches unity quadratically in 1/N. We also discuss this result in terms of the dimension of the encoding Hilbert space.

  13. PERFORMANCE OF THREE STAGE TURBO-EQUALIZATION-DECODING

    Institute of Scientific and Technical Information of China (English)

    Kazi Takpaya

    2003-01-01

    An increasing demand for high data rate transmission and protection over bandlimited channels with severe inter-symbol interference has resulted in a flurry of activity to improve channel equalization, In conjunction with equalization, channel coding-decoding can be employed to improve system performance. In this letter, the performance of the three stage turbo-equalization-decoding employing log maximum a posteriori probability is experimentally evaluated by a fading simulator. The BER is evaluated using various information sequence and interleaver sizes taking into account that the communication medium is a noisy inter symbol interference channel.

  14. Joint source/channel iterative arithmetic decoding with JPEG 2000 image transmission application

    Science.gov (United States)

    Zaibi, Sonia; Zribi, Amin; Pyndiah, Ramesh; Aloui, Nadia

    2012-12-01

    Motivated by recent results in Joint Source/Channel coding and decoding, we consider the decoding problem of Arithmetic Codes (AC). In fact, in this article we provide different approaches which allow one to unify the arithmetic decoding and error correction tasks. A novel length-constrained arithmetic decoding algorithm based on Maximum A Posteriori sequence estimation is proposed. The latter is based on soft-input decoding using a priori knowledge of the source-symbol sequence and the compressed bit-stream lengths. Performance in the case of transmission over an Additive White Gaussian Noise channel is evaluated in terms of Packet Error Rate. Simulation results show that the proposed decoding algorithm leads to significant performance gain while exhibiting very low complexity. The proposed soft input arithmetic decoder can also generate additional information regarding the reliability of the compressed bit-stream components. We consider the serial concatenation of the AC with a Recursive Systematic Convolutional Code, and perform iterative decoding. We show that, compared to tandem and to trellis-based Soft-Input Soft-Output decoding schemes, the proposed decoder exhibits the best performance/complexity tradeoff. Finally, the practical relevance of the presented iterative decoding system is validated under an image transmission scheme based on the JPEG 2000 standard and excellent results in terms of decoded image quality are obtained.

  15. 47 CFR 11.12 - Two-tone Attention Signal encoder and decoder.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Two-tone Attention Signal encoder and decoder... SYSTEM (EAS) General § 11.12 Two-tone Attention Signal encoder and decoder. Existing two-tone Attention... Attention Signal decoder will no longer be required and the two-tone Attention Signal will be used...

  16. Progressive Image Transmission Based on Joint Source-Channel Decoding Using Adaptive Sum-Product Algorithm

    Directory of Open Access Journals (Sweden)

    David G. Daut

    2007-03-01

    Full Text Available A joint source-channel decoding method is designed to accelerate the iterative log-domain sum-product decoding procedure of LDPC codes as well as to improve the reconstructed image quality. Error resilience modes are used in the JPEG2000 source codec making it possible to provide useful source decoded information to the channel decoder. After each iteration, a tentative decoding is made and the channel decoded bits are then sent to the JPEG2000 decoder. The positions of bits belonging to error-free coding passes are then fed back to the channel decoder. The log-likelihood ratios (LLRs of these bits are then modified by a weighting factor for the next iteration. By observing the statistics of the decoding procedure, the weighting factor is designed as a function of the channel condition. Results show that the proposed joint decoding methods can greatly reduce the number of iterations, and thereby reduce the decoding delay considerably. At the same time, this method always outperforms the nonsource controlled decoding method by up to 3 dB in terms of PSNR.

  17. Construction and decoding of matrix-product codes from nested codes

    DEFF Research Database (Denmark)

    Hernando, Fernando; Lally, Kristine; Ruano, Diego

    2009-01-01

    We consider matrix-product codes [C1 ... Cs] · A, where C1, ..., Cs  are nested linear codes and matrix A has full rank. We compute their minimum distance and provide a decoding algorithm when A is a non-singular by columns matrix. The decoding algorithm decodes up to half of the minimum distance....

  18. Progressive Image Transmission Based on Joint Source-Channel Decoding Using Adaptive Sum-Product Algorithm

    Directory of Open Access Journals (Sweden)

    Liu Weiliang

    2007-01-01

    Full Text Available A joint source-channel decoding method is designed to accelerate the iterative log-domain sum-product decoding procedure of LDPC codes as well as to improve the reconstructed image quality. Error resilience modes are used in the JPEG2000 source codec making it possible to provide useful source decoded information to the channel decoder. After each iteration, a tentative decoding is made and the channel decoded bits are then sent to the JPEG2000 decoder. The positions of bits belonging to error-free coding passes are then fed back to the channel decoder. The log-likelihood ratios (LLRs of these bits are then modified by a weighting factor for the next iteration. By observing the statistics of the decoding procedure, the weighting factor is designed as a function of the channel condition. Results show that the proposed joint decoding methods can greatly reduce the number of iterations, and thereby reduce the decoding delay considerably. At the same time, this method always outperforms the nonsource controlled decoding method by up to 3 dB in terms of PSNR.

  19. Homogeneous Interpolation Problem and Key Equation for Decoding Reed-Solomon Codes

    Institute of Scientific and Technical Information of China (English)

    忻鼎稼

    1994-01-01

    The concept of homogeneous interpolation problem (HIP) over fields is introduced.It is discovered that solving HIP over finite fields is equivalent to decoding Reed-Solomon (RS) codes.The Welch-Berlekamp algorithm of decoding RS codes is derived;besides,by introducing the concept of incomplete locator of error patterns,the algorithm called incomplete iterative decoding is established.

  20. Decoding the Long Noncoding RNA During Cardiac Maturation: A Roadmap for Functional Discovery.

    Science.gov (United States)

    Touma, Marlin; Kang, Xuedong; Zhao, Yan; Cass, Ashley A; Gao, Fuying; Biniwale, Reshma; Coppola, Giovanni; Xiao, Xinshu; Reemtsen, Brian; Wang, Yibin

    2016-10-01

    Cardiac maturation during perinatal transition of heart is critical for functional adaptation to hemodynamic load and nutrient environment. Perturbation in this process has major implications in congenital heart defects. Transcriptome programming during perinatal stages is an important information but incomplete in current literature, particularly, the expression profiles of the long noncoding RNAs (lncRNAs) are not fully elucidated. From comprehensive analysis of transcriptomes derived from neonatal mouse heart left and right ventricles, a total of 45 167 unique transcripts were identified, including 21 916 known and 2033 novel lncRNAs. Among these lncRNAs, 196 exhibited significant dynamic regulation along maturation process. By implementing parallel weighted gene co-expression network analysis of mRNA and lncRNA data sets, several lncRNA modules coordinately expressed in a developmental manner similar to protein coding genes, while few lncRNAs revealed chamber-specific patterns. Out of 2262 lncRNAs located within 50 kb of protein coding genes, 5% significantly correlate with the expression of their neighboring genes. The impact of Ppp1r1b-lncRNA on the corresponding partner gene Tcap was validated in cultured myoblasts. This concordant regulation was also conserved in human infantile hearts. Furthermore, the Ppp1r1b-lncRNA/Tcap expression ratio was identified as a molecular signature that differentiated congenital heart defect phenotypes. The study provides the first high-resolution landscape on neonatal cardiac lncRNAs and reveals their potential interaction with mRNA transcriptome during cardiac maturation. Ppp1r1b-lncRNA was identified as a regulator of Tcap expression, with dynamic interaction in postnatal cardiac development and congenital heart defects. © 2016 American Heart Association, Inc.

  1. TC81220F (HAWK) MPEG 2 system decoder LSI; MPEG2 system decoder LSI TC81220F (HAWK)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-03-01

    Satellite broadcasting, cable broadcasting, and ground wave broadcasting have been digitized gradually. In the video and audio data communication, the MPEG2 (Moving Picture Experts Group 2) technology for compression and extension is important. A system LSI that includes an MPEG2 decoder in a receiving set (Set Top Box) is required to each broadcasting. To deduce the system cost, Toshiba developed a TX3904 MCU (microcontroller) that controls the system, a transport processor that selects the packet-multiplexed data, and TC81220F (HAWK) that puts MPEG2 audio video decoders in one chip. (translated by NEDO)

  2. Polar Coding with CRC-Aided List Decoding

    Science.gov (United States)

    2015-08-01

    decoder estimates û1, . . . , ûN , one at a time, in order. For conve- nience, we introduce some non-standard notation. For any k ≤ N and any sequence of... recursive formula, but the true probability cannot be computed efficiently. The estimate differs from the true probability because the recursive formula

  3. A quantum algorithm for Viterbi decoding of classical convolutional codes

    Science.gov (United States)

    Grice, Jon R.; Meyer, David A.

    2015-07-01

    We present a quantum Viterbi algorithm (QVA) with better than classical performance under certain conditions. In this paper, the proposed algorithm is applied to decoding classical convolutional codes, for instance, large constraint length and short decode frames . Other applications of the classical Viterbi algorithm where is large (e.g., speech processing) could experience significant speedup with the QVA. The QVA exploits the fact that the decoding trellis is similar to the butterfly diagram of the fast Fourier transform, with its corresponding fast quantum algorithm. The tensor-product structure of the butterfly diagram corresponds to a quantum superposition that we show can be efficiently prepared. The quantum speedup is possible because the performance of the QVA depends on the fanout (number of possible transitions from any given state in the hidden Markov model) which is in general much less than . The QVA constructs a superposition of states which correspond to all legal paths through the decoding lattice, with phase as a function of the probability of the path being taken given received data. A specialized amplitude amplification procedure is applied one or more times to recover a superposition where the most probable path has a high probability of being measured.

  4. Complete ML Decoding orf the (73,45) PG Code

    DEFF Research Database (Denmark)

    Justesen, Jørn; Høholdt, Tom; Hjaltason, Johan

    2005-01-01

    Our recent proof of the completeness of decoding by list bit flipping is reviewed. The proof is based on an enumeration of all cosets of low weight in terms of their minimum weight and syndrome weight. By using a geometric description of the error patterns we characterize all remaining cosets....

  5. Name that tune: Decoding music from the listening brain

    NARCIS (Netherlands)

    Schaefer, R.S.; Farquhar, J.D.R.; Blokland, Y.M.; Sadakata, M.; Desain, P.W.M.

    2011-01-01

    In the current study we use electroencephalography (EEG) to detect heard music from the brain signal, hypothesizing that the time structure in music makes it especially suitable for decoding perception from EEG signals. While excluding music with vocals, we classified the perception of seven differe

  6. Spread codes and spread decoding in network coding

    OpenAIRE

    Manganiello, F; Gorla, E.; Rosenthal, J.

    2008-01-01

    In this paper we introduce the class of spread codes for the use in random network coding. Spread codes are based on the construction of spreads in finite projective geometry. The major contribution of the paper is an efficient decoding algorithm of spread codes up to half the minimum distance.

  7. The Effectiveness of Dictionary Examples in Decoding: The Case of ...

    African Journals Online (AJOL)

    rbr

    COBUILD English Language Dictionary, relies entirely on a corpus for its exam- ... corpus examples, while intermediate learners can learn from 'controlled' exam- ... learners' dictionaries, a possible indication of their difficulties with them. But .... tionary are mostly used for decoding rather than encoding linguistic activities.

  8. Relationships between grammatical encoding and decoding : an experimental psycholinguistic study

    NARCIS (Netherlands)

    Olsthoorn, Nomi Maria

    2007-01-01

    Although usually considered distinct processes, grammatical encoding and decoding have many theoretical and empirical commonalities. In two series of experiments relationships between the two processes are explored. The first series uses a dual task (edited reading aloud (ERA)) paradigm to test the

  9. Phonological Awareness and Decoding Skills in Deaf Adolescents

    Science.gov (United States)

    Gravenstede, L.

    2009-01-01

    This study investigated the phonological awareness skills of a group of deaf adolescents and how these skills correlated with decoding skills (single word and non-word reading) and receptive vocabulary. Twenty, congenitally profoundly deaf adolescents with at least average nonverbal cognitive skills were tested on a range of phonological awareness…

  10. Real Time Decoding of Color Symbol for Optical Positioning System

    Directory of Open Access Journals (Sweden)

    Abdul Waheed Malik

    2015-01-01

    Full Text Available This paper presents the design and real-time decoding of a color symbol that can be used as a reference marker for optical navigation. The designed symbol has a circular shape and is printed on paper using two distinct colors. This pair of colors is selected based on the highest achievable signal to noise ratio. The symbol is designed to carry eight bit information. Real time decoding of this symbol is performed using a heterogeneous combination of Field Programmable Gate Array (FPGA and a microcontroller. An image sensor having a resolution of 1600 by 1200 pixels is used to capture images of symbols in complex back‐ grounds. Dynamic image segmentation, component labeling and feature extraction was performed on the FPGA. The region of interest was further computed from the extracted features. Feature data belonging to the symbol was sent from the FPGA to the microcontroller. Image processing tasks are partitioned between the FPGA and microcontroller based on data intensity. Experiments were performed to verify the rotational independence of the symbols. The maximum distance between camera and symbol allowing for correct detection and decoding was analyzed. Experiments were also performed to analyze the number of generated image components and sub-pixel precision versus different light sources and intensities. The proposed hardware architecture can process up to 55 frames per second for accurate detection and decoding of symbols at two Megapixels resolution. The power consumption of the complete system is 342mw.

  11. Gradient Descent Bit Flipping Algorithms for Decoding LDPC Codes

    OpenAIRE

    Wadayama, Tadashi; Nakamura, Keisuke; Yagita, Masayuki; Funahashi, Yuuki; Usami, Shogo; Takumi, Ichi

    2007-01-01

    A novel class of bit-flipping (BF) algorithms for decoding low-density parity-check (LDPC) codes is presented. The proposed algorithms, which are called gradient descent bit flipping (GDBF) algorithms, can be regarded as simplified gradient descent algorithms. Based on gradient descent formulation, the proposed algorithms are naturally derived from a simple non-linear objective function.

  12. Name that tune: decoding music from the listening brain.

    NARCIS (Netherlands)

    Schaefer, R.S.; Farquhar, J.; Blokland, Y.M.; Sadakata, M.; Desain, P.

    2011-01-01

    In the current study we use electroencephalography (EEG) to detect heard music from the brain signal, hypothesizing that the time structure in music makes it especially suitable for decoding perception from EEG signals. While excluding music with vocals, we classified the perception of seven differe

  13. Real Time Decoding of Color Symbol for Optical Positioning System

    Directory of Open Access Journals (Sweden)

    Abdul Waheed Malik

    2015-01-01

    Full Text Available This paper presents the design and real-time decoding of a color symbol that can be used as a reference marker for optical navigation. The designed symbol has a circular shape and is printed on paper using two distinct colors. This pair of colors is selected based on the highest achievable signal to noise ratio. The symbol is designed to carry eight bit information. Real time decoding of this symbol is performed using a heterogeneous combination of Field Programmable Gate Array (FPGA and a microcontroller. An image sensor having a resolution of 1600 by 1200 pixels is used to capture images of symbols in complex backgrounds. Dynamic image segmentation, component labeling and feature extraction was performed on the FPGA. The region of interest was further computed from the extracted features. Feature data belonging to the symbol was sent from the FPGA to the microcontroller. Image processing tasks are partitioned between the FPGA and microcontroller based on data intensity. Experiments were performed to verify the rotational independence of the symbols. The maximum distance between camera and symbol allowing for correct detection and decoding was analyzed. Experiments were also performed to analyze the number of generated image components and sub-pixel precision versus different light sources and intensities. The proposed hardware architecture can process up to 55 frames per second for accurate detection and decoding of symbols at two Megapixels resolution. The power consumption of the complete system is 342mw.

  14. Decoding a combined amplitude modulated and frequency modulated signal

    DEFF Research Database (Denmark)

    2015-01-01

    The present disclosure relates to a method for decoding a combined AM/FM encoded signal, comprising the steps of: combining said encoded optical signal with light from a local oscillator configured with a local oscillator frequency; converting the combined local oscillator and encoded optical sig...

  15. Method for Veterbi decoding of large constraint length convolutional codes

    Science.gov (United States)

    Hsu, In-Shek; Truong, Trieu-Kie; Reed, Irving S.; Jing, Sun

    1988-05-01

    A new method of Viterbi decoding of convolutional codes lends itself to a pipline VLSI architecture using a single sequential processor to compute the path metrics in the Viterbi trellis. An array method is used to store the path information for NK intervals where N is a number, and K is constraint length. The selected path at the end of each NK interval is then selected from the last entry in the array. A trace-back method is used for returning to the beginning of the selected path back, i.e., to the first time unit of the interval NK to read out the stored branch metrics of the selected path which correspond to the message bits. The decoding decision made in this way is no longer maximum likelihood, but can be almost as good, provided that constraint length K in not too small. The advantage is that for a long message, it is not necessary to provide a large memory to store the trellis derived information until the end of the message to select the path that is to be decoded; the selection is made at the end of every NK time unit, thus decoding a long message in successive blocks.

  16. Name that tune: Decoding music from the listening brain

    NARCIS (Netherlands)

    Schaefer, R.S.; Farquhar, J.D.R.; Blokland, Y.M.; Sadakata, M.; Desain, P.W.M.

    2011-01-01

    In the current study we use electroencephalography (EEG) to detect heard music from the brain signal, hypothesizing that the time structure in music makes it especially suitable for decoding perception from EEG signals. While excluding music with vocals, we classified the perception of seven

  17. Name that tune: decoding music from the listening brain.

    NARCIS (Netherlands)

    Schaefer, R.S.; Farquhar, J.; Blokland, Y.M.; Sadakata, M.; Desain, P.

    2011-01-01

    In the current study we use electroencephalography (EEG) to detect heard music from the brain signal, hypothesizing that the time structure in music makes it especially suitable for decoding perception from EEG signals. While excluding music with vocals, we classified the perception of seven

  18. Error Locked Encoder and Decoder for Nanomemory Application

    Directory of Open Access Journals (Sweden)

    Y. Sharath

    2014-03-01

    Full Text Available Memory cells have been protected from soft errors for more than a decade; due to the increase in soft error rate in logic circuits, the encoder and decoder circuitry around the memory blocks have become susceptible to soft errors as well and must also be protected. We introduce a new approach to design fault-secure encoder and decoder circuitry for memory designs. The key novel contribution of this paper is identifying and defining a new class of error-correcting codes whose redundancy makes the design of fault-secure detectors (FSD particularly simple. We further quantify the importance of protecting encoder and decoder circuitry against transient errors, illustrating a scenario where the system failure rate (FIT is dominated by the failure rate of the encoder and decoder. We prove that Euclidean Geometry Low-Density Parity-Check (EG-LDPC codes have the fault-secure detector capability. Using some of the smaller EG-LDPC codes, we can tolerate bit or nanowire defect rates of 10% and fault rates of 10-18 upsets/device/cycle, achieving a FIT rate at or below one for the entire memory system and a memory density of 1011 bit/cm with nanowire pitch of 10 nm for memory blocks of 10 Mb or larger. Larger EG-LDPC codes can achieve even higher reliability and lower area overhead.

  19. Decoding the Disciplines: An Approach to Scientific Thinking

    Science.gov (United States)

    Pinnow, Eleni

    2016-01-01

    The Decoding the Disciplines methodology aims to teach students to think like experts in discipline-specific tasks. The central aspect of the methodology is to identify a bottleneck in the course content: a particular topic that a substantial number of students struggle to master. The current study compared the efficacy of standard lecture and…

  20. Sub-quadratic decoding of one-point hermitian codes

    DEFF Research Database (Denmark)

    Nielsen, Johan Sebastian Rosenkilde; Beelen, Peter

    2015-01-01

    We present the first two sub-quadratic complexity decoding algorithms for one-point Hermitian codes. The first is based on a fast realization of the Guruswami-Sudan algorithm using state-of-the-art algorithms from computer algebra for polynomial-ring matrix minimization. The second is a power...

  1. The Fluid Reading Primer: Animated Decoding Support for Emergent Readers.

    Science.gov (United States)

    Zellweger, Polle T.; Mackinlay, Jock D.

    A prototype application called the Fluid Reading Primer was developed to help emergent readers with the process of decoding written words into their spoken forms. The Fluid Reading Primer is part of a larger research project called Fluid Documents, which is exploring the use of interactive animation of typography to show additional information in…

  2. Decoding the Role of Glycans in Malaria

    Directory of Open Access Journals (Sweden)

    Pollyanna S. Gomes

    2017-06-01

    Full Text Available Complications arising from malaria are a concern for public health authorities worldwide, since the annual caseload in humans usually exceeds millions. Of more than 160 species of Plasmodium, only 4 infect humans, with the most severe cases ascribed to Plasmodium falciparum and the most prevalent to Plasmodium vivax. Over the past 70 years, since World War II, when the first antimalarial drugs were widely used, many efforts have been made to combat this disease, including vectorial control, new drug discoveries and genetic and molecular approaches. Molecular approaches, such as glycobiology, may lead to new therapeutic targets (both in the host and the parasites, since all interactions are mediated by carbohydrates or glycan moieties decorating both cellular surfaces from parasite and host cells. In this review, we address the carbohydrate-mediated glycobiology that directly affects Plasmodium survival or host resistance.

  3. A Novel Decoder for Unknown Diversity Channels Employing Space-Time Codes

    Directory of Open Access Journals (Sweden)

    Erez Elona

    2002-01-01

    Full Text Available We suggest new decoding techniques for diversity channels employing space time codes (STC when the channel coefficients are unknown to both transmitter and receiver. Most of the existing decoders for unknown diversity channels employ training sequence in order to estimate the channel. These decoders use the estimates of the channel coefficients in order to perform maximum likelihood (ML decoding. We suggest an efficient implementation of the generalized likelihood ratio test (GLRT algorithm that improves the performance with only slight increase in complexity. We also suggest an energy weighted decoder (EWD that shows additional improvement without further increase in the computational complexity.

  4. On Pseudocodewords and Decision Regions of Linear Programming Decoding of HDPC Codes

    CERN Document Server

    Lifshitz, Asi

    2011-01-01

    In this paper we explore the decision regions of Linear Programming (LP) decoding. We compare the decision regions of an LP decoder, a Belief Propagation (BP) decoder and the optimal Maximum Likelihood (ML) decoder. We study the effect of minimal-weight pseudocodewords on LP decoding. We present global optimization as a method for finding the minimal pseudoweight of a given code as well as the number of minimal-weight generators. We present a complete pseudoweight distribution for the [24; 12; 8] extended Golay code, and provide justifications of why the pseudoweight distribution alone cannot be used for obtaining a tight upper bound on the error probability.

  5. New concatenated soft decoding of Reed-Solomon codes with lower complexities

    Institute of Scientific and Technical Information of China (English)

    BIAN Yin-bing; FENG Guang-zeng

    2009-01-01

    To improve error-correcting performance, an iterative concatenated soft decoding algorithm for Reed-Solomon (RS) codes is presented in this article. This algorithm brings both complexity as well as advantages in performance over presently popular sott decoding algorithms. The proposed algorithm consists of two powerful soft decoding techniques, adaptive belief propagation (ABP) and box and match algorithm (BMA), which are serially concatenated by the accumulated log-likelihood ratio (ALLR).Simulation results show that, compared with ABP and ABP-BMA algorithms, the proposed algorithm can bring more decoding gains and a better tradeoffbetween the decoding performance and complexity.

  6. On Lattice Sequential Decoding for Large MIMO Systems

    KAUST Repository

    Ali, Konpal S.

    2014-04-01

    Due to their ability to provide high data rates, Multiple-Input Multiple-Output (MIMO) wireless communication systems have become increasingly popular. Decoding of these systems with acceptable error performance is computationally very demanding. In the case of large overdetermined MIMO systems, we employ the Sequential Decoder using the Fano Algorithm. A parameter called the bias is varied to attain different performance-complexity trade-offs. Low values of the bias result in excellent performance but at the expense of high complexity and vice versa for higher bias values. We attempt to bound the error by bounding the bias, using the minimum distance of a lattice. Also, a particular trend is observed with increasing SNR: a region of low complexity and high error, followed by a region of high complexity and error falling, and finally a region of low complexity and low error. For lower bias values, the stages of the trend are incurred at lower SNR than for higher bias values. This has the important implication that a low enough bias value, at low to moderate SNR, can result in low error and low complexity even for large MIMO systems. Our work is compared against Lattice Reduction (LR) aided Linear Decoders (LDs). Another impressive observation for low bias values that satisfy the error bound is that the Sequential Decoder\\'s error is seen to fall with increasing system size, while it grows for the LR-aided LDs. For the case of large underdetermined MIMO systems, Sequential Decoding with two preprocessing schemes is proposed – 1) Minimum Mean Square Error Generalized Decision Feedback Equalization (MMSE-GDFE) preprocessing 2) MMSE-GDFE preprocessing, followed by Lattice Reduction and Greedy Ordering. Our work is compared against previous work which employs Sphere Decoding preprocessed using MMSE-GDFE, Lattice Reduction and Greedy Ordering. For the case of large systems, this results in high complexity and difficulty in choosing the sphere radius. Our schemes

  7. Sums of Spike Waveform Features for Motor Decoding

    Directory of Open Access Journals (Sweden)

    Jie Li

    2017-07-01

    Full Text Available Traditionally, the key step before decoding motor intentions from cortical recordings is spike sorting, the process of identifying which neuron was responsible for an action potential. Recently, researchers have started investigating approaches to decoding which omit the spike sorting step, by directly using information about action potentials' waveform shapes in the decoder, though this approach is not yet widespread. Particularly, one recent approach involves computing the moments of waveform features and using these moment values as inputs to decoders. This computationally inexpensive approach was shown to be comparable in accuracy to traditional spike sorting. In this study, we use offline data recorded from two Rhesus monkeys to further validate this approach. We also modify this approach by using sums of exponentiated features of spikes, rather than moments. Our results show that using waveform feature sums facilitates significantly higher hand movement reconstruction accuracy than using waveform feature moments, though the magnitudes of differences are small. We find that using the sums of one simple feature, the spike amplitude, allows better offline decoding accuracy than traditional spike sorting by expert (correlation of 0.767, 0.785 vs. 0.744, 0.738, respectively, for two monkeys, average 16% reduction in mean-squared-error, as well as unsorted threshold crossings (0.746, 0.776; average 9% reduction in mean-squared-error. Our results suggest that the sums-of-features framework has potential as an alternative to both spike sorting and using unsorted threshold crossings, if developed further. Also, we present data comparing sorted vs. unsorted spike counts in terms of offline decoding accuracy. Traditional sorted spike counts do not include waveforms that do not match any template (“hash”, but threshold crossing counts do include this hash. On our data and in previous work, hash contributes to decoding accuracy. Thus, using the

  8. Fast multiple run_before decoding method for efficient implementation of an H.264/advanced video coding context-adaptive variable length coding decoder

    Science.gov (United States)

    Ki, Dae Wook; Kim, Jae Ho

    2013-07-01

    We propose a fast new multiple run_before decoding method in context-adaptive variable length coding (CAVLC). The transform coefficients are coded using CAVLC, in which the run_before symbols are generated for a 4×4 block input. To speed up the CAVLC decoding, the run_before symbols need to be decoded in parallel. We implemented a new CAVLC table for simultaneous decoding of up to three run_befores. The simulation results show a Total Speed-up Factor of 205%˜144% over various resolutions and quantization steps.

  9. Multi-stage decoding for multi-level block modulation codes

    Science.gov (United States)

    Lin, Shu

    1991-01-01

    In this paper, we investigate various types of multi-stage decoding for multi-level block modulation codes, in which the decoding of a component code at each stage can be either soft-decision or hard-decision, maximum likelihood or bounded-distance. Error performance of codes is analyzed for a memoryless additive channel based on various types of multi-stage decoding, and upper bounds on the probability of an incorrect decoding are derived. Based on our study and computation results, we find that, if component codes of a multi-level modulation code and types of decoding at various stages are chosen properly, high spectral efficiency and large coding gain can be achieved with reduced decoding complexity. In particular, we find that the difference in performance between the suboptimum multi-stage soft-decision maximum likelihood decoding of a modulation code and the single-stage optimum decoding of the overall code is very small: only a fraction of dB loss in SNR at the probability of an incorrect decoding for a block of 10(exp -6). Multi-stage decoding of multi-level modulation codes really offers a way to achieve the best of three worlds, bandwidth efficiency, coding gain, and decoding complexity.

  10. A Generalization Belief Propagation Decoding Algorithm for Polar Codes Based on Particle Swarm Optimization

    Directory of Open Access Journals (Sweden)

    Yingxian Zhang

    2014-01-01

    Full Text Available We propose a generalization belief propagation (BP decoding algorithm based on particle swarm optimization (PSO to improve the performance of the polar codes. Through the analysis of the existing BP decoding algorithm, we first introduce a probability modifying factor to each node of the BP decoder, so as to enhance the error correcting capacity of the decoding. Then, we generalize the BP decoding algorithm based on these modifying factors and drive the probability update equations for the proposed decoding. Based on the new probability update equations, we show the intrinsic relationship of the existing decoding algorithms. Finally, in order to achieve the best performance, we formulate an optimization problem to find the optimal probability modifying factors for the proposed decoding algorithm. Furthermore, a method based on the modified PSO algorithm is also introduced to solve that optimization problem. Numerical results show that the proposed generalization BP decoding algorithm achieves better performance than that of the existing BP decoding, which suggests the effectiveness of the proposed decoding algorithm.

  11. Decoding bipedal locomotion from the rat sensorimotor cortex

    Science.gov (United States)

    Rigosa, J.; Panarese, A.; Dominici, N.; Friedli, L.; van den Brand, R.; Carpaneto, J.; DiGiovanna, J.; Courtine, G.; Micera, S.

    2015-10-01

    Objective. Decoding forelimb movements from the firing activity of cortical neurons has been interfaced with robotic and prosthetic systems to replace lost upper limb functions in humans. Despite the potential of this approach to improve locomotion and facilitate gait rehabilitation, decoding lower limb movement from the motor cortex has received comparatively little attention. Here, we performed experiments to identify the type and amount of information that can be decoded from neuronal ensemble activity in the hindlimb area of the rat motor cortex during bipedal locomotor tasks. Approach. Rats were trained to stand, step on a treadmill, walk overground and climb staircases in a bipedal posture. To impose this gait, the rats were secured in a robotic interface that provided support against the direction of gravity and in the mediolateral direction, but behaved transparently in the forward direction. After completion of training, rats were chronically implanted with a micro-wire array spanning the left hindlimb motor cortex to record single and multi-unit activity, and bipolar electrodes into 10 muscles of the right hindlimb to monitor electromyographic signals. Whole-body kinematics, muscle activity, and neural signals were simultaneously recorded during execution of the trained tasks over multiple days of testing. Hindlimb kinematics, muscle activity, gait phases, and locomotor tasks were decoded using offline classification algorithms. Main results. We found that the stance and swing phases of gait and the locomotor tasks were detected with accuracies as robust as 90% in all rats. Decoded hindlimb kinematics and muscle activity exhibited a larger variability across rats and tasks. Significance. Our study shows that the rodent motor cortex contains useful information for lower limb neuroprosthetic development. However, brain-machine interfaces estimating gait phases or locomotor behaviors, instead of continuous variables such as limb joint positions or speeds

  12. NEW ITERATIVE SUPER-TRELLIS DECODING WITH SOURCE A PRIORI INFORMATION FOR VLCS WITH TURBO CODES

    Institute of Scientific and Technical Information of China (English)

    Liu Jianjun; Tu Guofang; Wu Weiren

    2007-01-01

    A novel Joint Source and Channel Decoding (JSCD) scheme for Variable Length Codes (VLCs) concatenated with turbo codes utilizing a new super-trellis decoding algorithm is presented in this letter. The basic idea of our decoding algorithm is that source a priori information with the form of bit transition probabilities corresponding to the VLC tree can be derived directly from sub-state transitions in new composite-state represented super-trellis. A Maximum Likelihood (ML) decoding algorithm for VLC sequence estimations based on the proposed super-trellis is also described. Simulation results show that the new iterative decoding scheme can obtain obvious encoding gain especially for Reversible Variable Length Codes (RVLCs), when compared with the classical separated turbo decoding and the previous joint decoding not considering source statistical characteristics.

  13. Trellis-Based Check Node Processing for Low-Complexity Nonbinary LP Decoding

    CERN Document Server

    Punekar, Mayur

    2011-01-01

    Linear Programming (LP) decoding is emerging as an attractive alternative to decode Low-Density Parity-Check (LDPC) codes. However, the earliest LP decoders proposed for binary and nonbinary LDPC codes are not suitable for use at moderate and large code lengths. To overcome this problem, Vontobel et al. developed an iterative Low-Complexity LP (LCLP) decoding algorithm for binary LDPC codes. The variable and check node calculations of binary LCLP decoding algorithm are related to those of binary Belief Propagation (BP). The present authors generalized this work to derive an iterative LCLP decoding algorithm for nonbinary linear codes. Contrary to binary LCLP, the variable and check node calculations of this algorithm are in general different from that of nonbinary BP. The overall complexity of nonbinary LCLP decoding is linear in block length; however the complexity of its check node calculations is exponential in the check node degree. In this paper, we propose a modified BCJR algorithm for efficient check n...

  14. Iterative decoding of Generalized Parallel Concatenated Block codes using cyclic permutations

    Directory of Open Access Journals (Sweden)

    Hamid Allouch

    2012-09-01

    Full Text Available Iterative decoding techniques have gain popularity due to their performance and their application in most communications systems. In this paper, we present a new application of our iterative decoder on the GPCB (Generalized Parallel Concatenated Block codes which uses cyclic permutations. We introduce a new variant of the component decoder. After extensive simulation; the obtained result is very promising compared with several existing methods. We evaluate the effects of various parameters component codes, interleaver size, block size, and the number of iterations. Three interesting results are obtained; the first one is that the performances in terms of BER (Bit Error Rate of the new constituent decoder are relatively similar to that of original one. Secondly our turbo decoding outperforms another turbo decoder for some linear block codes. Thirdly the proposed iterative decoding of GPCB-BCH (75, 51 is about 2.1dB from its Shannon limit.

  15. Low Complexity Approach for High Throughput Belief-Propagation based Decoding of LDPC Codes

    Directory of Open Access Journals (Sweden)

    BOT, A.

    2013-11-01

    Full Text Available The paper proposes a low complexity belief propagation (BP based decoding algorithm for LDPC codes. In spite of the iterative nature of the decoding process, the proposed algorithm provides both reduced complexity and increased BER performances as compared with the classic min-sum (MS algorithm, generally used for hardware implementations. Linear approximations of check-nodes update function are used in order to reduce the complexity of the BP algorithm. Considering this decoding approach, an FPGA based hardware architecture is proposed for implementing the decoding algorithm, aiming to increase the decoder throughput. FPGA technology was chosen for the LDPC decoder implementation, due to its parallel computation and reconfiguration capabilities. The obtained results show improvements regarding decoding throughput and BER performances compared with state-of-the-art approaches.

  16. Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes. Part 3; A Recursive Maximum Likelihood Decoding

    Science.gov (United States)

    Lin, Shu; Fossorier, Marc

    1998-01-01

    The Viterbi algorithm is indeed a very simple and efficient method of implementing the maximum likelihood decoding. However, if we take advantage of the structural properties in a trellis section, other efficient trellis-based decoding algorithms can be devised. Recently, an efficient trellis-based recursive maximum likelihood decoding (RMLD) algorithm for linear block codes has been proposed. This algorithm is more efficient than the conventional Viterbi algorithm in both computation and hardware requirements. Most importantly, the implementation of this algorithm does not require the construction of the entire code trellis, only some special one-section trellises of relatively small state and branch complexities are needed for constructing path (or branch) metric tables recursively. At the end, there is only one table which contains only the most likely code-word and its metric for a given received sequence r = (r(sub 1), r(sub 2),...,r(sub n)). This algorithm basically uses the divide and conquer strategy. Furthermore, it allows parallel/pipeline processing of received sequences to speed up decoding.

  17. NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities.

    Science.gov (United States)

    da Rocha, Edroaldo Lummertz; Ung, Choong Yong; McGehee, Cordelia D; Correia, Cristina; Li, Hu

    2016-06-02

    The sequential chain of interactions altering the binary state of a biomolecule represents the 'information flow' within a cellular network that determines phenotypic properties. Given the lack of computational tools to dissect context-dependent networks and gene activities, we developed NetDecoder, a network biology platform that models context-dependent information flows using pairwise phenotypic comparative analyses of protein-protein interactions. Using breast cancer, dyslipidemia and Alzheimer's disease as case studies, we demonstrate NetDecoder dissects subnetworks to identify key players significantly impacting cell behaviour specific to a given disease context. We further show genes residing in disease-specific subnetworks are enriched in disease-related signalling pathways and information flow profiles, which drive the resulting disease phenotypes. We also devise a novel scoring scheme to quantify key genes-network routers, which influence many genes, key targets, which are influenced by many genes, and high impact genes, which experience a significant change in regulation. We show the robustness of our results against parameter changes. Our network biology platform includes freely available source code (http://www.NetDecoder.org) for researchers to explore genome-wide context-dependent information flow profiles and key genes, given a set of genes of particular interest and transcriptome data. More importantly, NetDecoder will enable researchers to uncover context-dependent drug targets.

  18. Optimal Threshold-Based Multi-Trial Error/Erasure Decoding with the Guruswami-Sudan Algorithm

    CERN Document Server

    Senger, Christian; Bossert, Martin; Zyablov, Victor V

    2011-01-01

    Traditionally, multi-trial error/erasure decoding of Reed-Solomon (RS) codes is based on Bounded Minimum Distance (BMD) decoders with an erasure option. Such decoders have error/erasure tradeoff factor L=2, which means that an error is twice as expensive as an erasure in terms of the code's minimum distance. The Guruswami-Sudan (GS) list decoder can be considered as state of the art in algebraic decoding of RS codes. Besides an erasure option, it allows to adjust L to values in the range 1=1 times. We show that BMD decoders with z_BMD decoding trials can result in lower residual codeword error probability than GS decoders with z_GS trials, if z_BMD is only slightly larger than z_GS. This is of practical interest since BMD decoders generally have lower computational complexity than GS decoders.

  19. Decode-and-Forward Based Differential Modulation for Cooperative Communication System with Unitary and Non-Unitary Constellations

    CERN Document Server

    Bhatnagar, Manav R

    2012-01-01

    In this paper, we derive a maximum likelihood (ML) decoder of the differential data in a decode-and-forward (DF) based cooperative communication system utilizing uncoded transmissions. This decoder is applicable to complex-valued unitary and non-unitary constellations suitable for differential modulation. The ML decoder helps in improving the diversity of the DF based differential cooperative system using an erroneous relaying node. We also derive a piecewise linear (PL) decoder of the differential data transmitted in the DF based cooperative system. The proposed PL decoder significantly reduces the decoding complexity as compared to the proposed ML decoder without any significant degradation in the receiver performance. Existing ML and PL decoders of the differentially modulated uncoded data in the DF based cooperative communication system are only applicable to binary modulated signals like binary phase shift keying (BPSK) and binary frequency shift keying (BFSK), whereas, the proposed decoders are applicab...

  20. Coupled Receiver/Decoders for Low-Rate Turbo Codes

    Science.gov (United States)

    Hamkins, Jon; Divsalar, Dariush

    2005-01-01

    been proposed for receiving weak single- channel phase-modulated radio signals bearing low-rate-turbo-coded binary data. Originally intended for use in receiving telemetry signals from distant spacecraft, the proposed receiver/ decoders may also provide enhanced reception in mobile radiotelephone systems. A radio signal of the type to which the proposal applies comprises a residual carrier signal and a phase-modulated data signal. The residual carrier signal is needed as a phase reference for demodulation as a prerequisite to decoding. Low-rate turbo codes afford high coding gains and thereby enable the extraction of data from arriving radio signals that might otherwise be too weak. In the case of a conventional receiver, if the signal-to-noise ratio (specifically, the symbol energy to one-sided noise power spectral density) of the arriving signal is below approximately 0 dB, then there may not be enough energy per symbol to enable the receiver to recover properly the carrier phase. One could solve the problem at the transmitter by diverting some power from the data signal to the residual carrier. A better solution . a coupled receiver/decoder according to the proposal . could reduce the needed amount of residual carrier power. In all that follows, it is to be understood that all processing would be digital and the incoming signals to be processed would be, more precisely, outputs of analog-to-digital converters that preprocess the residual carrier and data signals at a rate of multiple samples per symbol. The upper part of the figure depicts a conventional receiving system, in which the receiver and decoder are uncoupled, and which is also called a non-data-aided system because output data from the decoder are not used in the receiver to aid in recovering the carrier phase. The receiver tracks the carrier phase from the residual carrier signal and uses the carrier phase to wipe phase noise off the data signal. The receiver typically includes a phase-locked loop

  1. Usability of Discovery Portals

    NARCIS (Netherlands)

    Bulens, J.D.; Vullings, L.A.E.; Houtkamp, J.M.; Vanmeulebrouk, B.

    2013-01-01

    As INSPIRE progresses to be implemented in the EU, many new discovery portals are built to facilitate finding spatial data. Currently the structure of the discovery portals is determined by the way spatial data experts like to work. However, we argue that the main target group for discovery portals

  2. Usability of Discovery Portals

    NARCIS (Netherlands)

    Bulens, J.D.; Vullings, L.A.E.; Houtkamp, J.M.; Vanmeulebrouk, B.

    2013-01-01

    As INSPIRE progresses to be implemented in the EU, many new discovery portals are built to facilitate finding spatial data. Currently the structure of the discovery portals is determined by the way spatial data experts like to work. However, we argue that the main target group for discovery portals

  3. Performance-complexity tradeoff in sequential decoding for the unconstrained AWGN channel

    KAUST Repository

    Abediseid, Walid

    2013-06-01

    In this paper, the performance limits and the computational complexity of the lattice sequential decoder are analyzed for the unconstrained additive white Gaussian noise channel. The performance analysis available in the literature for such a channel has been studied only under the use of the minimum Euclidean distance decoder that is commonly referred to as the lattice decoder. Lattice decoders based on solutions to the NP-hard closest vector problem are very complex to implement, and the search for low complexity receivers for the detection of lattice codes is considered a challenging problem. However, the low computational complexity advantage that sequential decoding promises, makes it an alternative solution to the lattice decoder. In this work, we characterize the performance and complexity tradeoff via the error exponent and the decoding complexity, respectively, of such a decoder as a function of the decoding parameter - the bias term. For the above channel, we derive the cut-off volume-to-noise ratio that is required to achieve a good error performance with low decoding complexity. © 2013 IEEE.

  4. Memory bandwidth efficient two-layer reduced-resolution decoding of high-definition video

    Science.gov (United States)

    Comer, Mary L.

    2000-12-01

    This paper addresses the problem of efficiently decoding high- definition (HD) video for display at a reduced resolution. The decoder presented in this paper is intended for applications that are constrained not only in memory size, but also in peak memory bandwidth. This is the case, for example, during decoding of a high-definition television (HDTV) channel for picture-in-picture (PIP) display, if the reduced resolution PIP-channel decoder is sharing memory with the full-resolution main-channel decoder. The most significant source of video quality degradation in a reduced-resolution decoder is prediction drift, which is caused by the mismatch between the full-resolution reference frames used by the encoder and the subsampled reference frames used by the decoder. to mitigate the visually annoying effects of prediction drift, the decoder described in this paper operates at two different resolutions -- a lower resolution for B pictures, which do not contribute to prediction drift and a higher resolution for I and P pictures. This means that the motion-compensation unit (MCU) essentially operates at the higher resolution, but the peak memory bandwidth is the same as that required to decode at the lower resolution. Storage of additional data, representing the higher resolution for I and P pictures, requires a relatively small amount of additional memory as compared to decoding at the lower resolution. Experimental results will demonstrate the improvement in video quality achieved by the addition of the higher-resolution data in forming predictions for P pictures.

  5. Word decoding development in incremental phonics instruction in a transparent orthography.

    Science.gov (United States)

    Schaars, Moniek M H; Segers, Eliane; Verhoeven, Ludo

    2017-01-01

    The present longitudinal study aimed to investigate the development of word decoding skills during incremental phonics instruction in Dutch as a transparent orthography. A representative sample of 973 Dutch children in the first grade (Mage  = 6;1, SD = 0;5) was exposed to incremental subsets of Dutch grapheme-phoneme correspondences during 6 consecutive blocks of 3 weeks of phonics instruction. Children's accuracy and efficiency of curriculum embedded word decoding were assessed after each incremental block, followed by a standardized word decoding measurement. Precursor measures of rapid naming, short-term memory, vocabulary, phonological awareness, and letter knowledge were assessed by the end of kindergarten and subsequently related to the word decoding efficiency in the first grade. The results showed that from the very beginning, children attained ceiling levels of decoding accuracy, whereas their efficiency scores increased despite the incremental character of the consecutive decoding assessments embedded in the curriculum. Structural equation modelling demonstrated high stability of the individual differences assessed by word decoding efficiency during phonics instruction during the first 5 months of the first grade. Curriculum embedded word decoding was highly related to standardized word decoding after phonics instruction was completed. Finally, early literacy and lexical retrieval, and to a lesser extent verbal and visual short term memory, predicted the first fundamental processes of mastering word decoding skills.

  6. STACK DECODING OF LINEAR BLOCK CODES FOR DISCRETE MEMORYLESS CHANNEL USING TREE DIAGRAM

    Directory of Open Access Journals (Sweden)

    H. Prashantha Kumar

    2012-03-01

    Full Text Available The boundaries between block and convolutional codes have become diffused after recent advances in the understanding of the trellis structure of block codes and the tail-biting structure of some convolutional codes. Therefore, decoding algorithms traditionally proposed for decoding convolutional codes have been applied for decoding certain classes of block codes. This paper presents the decoding of block codes using tree structure. Many good block codes are presently known. Several of them have been used in applications ranging from deep space communication to error control in storage systems. But the primary difficulty with applying Viterbi or BCJR algorithms to decode of block codes is that, even though they are optimum decoding methods, the promised bit error rates are not achieved in practice at data rates close to capacity. This is because the decoding effort is fixed and grows with block length, and thus only short block length codes can be used. Therefore, an important practical question is whether a suboptimal realizable soft decision decoding method can be found for block codes. A noteworthy result which provides a partial answer to this question is described in the following sections. This result of near optimum decoding will be used as motivation for the investigation of different soft decision decoding methods for linear block codes which can lead to the development of efficient decoding algorithms. The code tree can be treated as an expanded version of the trellis, where every path is totally distinct from every other path. We have derived the tree structure for (8, 4 and (16, 11 extended Hamming codes and have succeeded in implementing the soft decision stack algorithm to decode them. For the discrete memoryless channel, gains in excess of 1.5dB at a bit error rate of 10-5 with respect to conventional hard decision decoding are demonstrated for these codes.

  7. Decoding of Convolutional Codes over the Erasure Channel

    CERN Document Server

    Tomás, Virtudes; Smarandache, Roxana

    2010-01-01

    In this paper we study the decoding capabilities of convolutional codes over the erasure channel. Of special interest will be maximum distance profile (MDP) convolutional codes. These are codes which have a maximum possible column distance increase. We show how this strong minimum distance condition of MDP convolutional codes help us to solve error situations that maximum distance separable (MDS) block codes fail to solve. Towards this goal, we define two subclasses of MDP codes: reverse-MDP convolutional codes and complete-MDP convolutional codes. Reverse-MDP codes have the capability to recover a maximum number of erasures using an algorithm which runs backward in time. Complete-MDP convolutional codes are both MDP and reverse-MDP codes. They are capable to recover the state of the decoder under the mildest condition. We show that complete-MDP convolutional codes perform in certain sense better than MDS block codes of the same rate over the erasure channel.

  8. Reaction Decoder Tool (RDT): extracting features from chemical reactions

    Science.gov (United States)

    Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W.; Holliday, Gemma L.; Steinbeck, Christoph; Thornton, Janet M.

    2016-01-01

    Summary: Extracting chemical features like Atom–Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. Availability and implementation: This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder Contact: asad@ebi.ac.uk or s9asad@gmail.com PMID:27153692

  9. Reaction Decoder Tool (RDT): extracting features from chemical reactions.

    Science.gov (United States)

    Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

    2016-07-01

    Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.

  10. Design And Analysis Of Low Power Hierarchical Decoder

    Directory of Open Access Journals (Sweden)

    Abhinav Singh

    2012-11-01

    Full Text Available Due to the high degree of miniaturization possible today in semiconductor technology, the size and complexity of designs that may be implemented in hardware has increased dramatically. Process scaling has been used in the miniaturization process to reduce the area needed for logic functions in an effort to lower the product costs. Precharged Complementary Metal Oxide Semiconductor (CMOS domino logic techniques may be applied to functional blocks to reduce power. Domino logic forms an attractive design style for high performance designs since its low switching threshold and reduced transistor count leads to fast and area efficient circuit implementations. In this paper all the necessary components required to form a 5-to-32 bit decoder using domino logic are designed to perform different analysis at 180nm & 350 nm technologies. Decoderimplemented through domino logic is compared to static decoder.

  11. Codes on the Klein quartic, ideals, and decoding

    DEFF Research Database (Denmark)

    Hansen, Johan P.

    1987-01-01

    descriptions as left ideals in the group-algebra GF(2^{3})[G]. This description allows for easy decoding. For instance, in the case of the single error correcting code of length21and dimension16with minimal distance3. decoding is obtained by multiplication with an idempotent in the group algebra.......A sequence of codes with particular symmetries and with large rates compared to their minimal distances is constructed over the field GF(2^{3}). In the sequence there is, for instance, a code of length 21 and dimension10with minimal distance9, and a code of length21and dimension16with minimal...... distance3. The codes are constructed from algebraic geometry using the dictionary between coding theory and algebraic curves over finite fields established by Goppa. The curve used in the present work is the Klein quartic. This curve has the maximal number of rational points over GF(2^{3})allowed by Serre...

  12. Soft decoding a self-dual (48, 24; 12) code

    Science.gov (United States)

    Solomon, G.

    1993-01-01

    A self-dual (48,24;12) code comes from restricting a binary cyclic (63,18;36) code to a 6 x 7 matrix, adding an eighth all-zero column, and then adjoining six dimensions to this extended 6 x 8 matrix. These six dimensions are generated by linear combinations of row permutations of a 6 x 8 matrix of weight 12, whose sums of rows and columns add to one. A soft decoding using these properties and approximating maximum likelihood is presented here. This is preliminary to a possible soft decoding of the box (72,36;15) code that promises a 7.7-dB theoretical coding under maximum likelihood.

  13. Computational Complexity of Decoding Orthogonal Space-Time Block Codes

    CERN Document Server

    Ayanoglu, Ender; Karipidis, Eleftherios

    2009-01-01

    The computational complexity of optimum decoding for an orthogonal space-time block code G satisfying the orthogonality property that the Hermitian transpose of G multiplied by G is equal to a constant c times the sum of the squared symbols of the code times an identity matrix, where c is a positive integer is quantified. Four equivalent techniques of optimum decoding which have the same computational complexity are specified. Modifications to the basic formulation in special cases are calculated and illustrated by means of examples. This paper corrects and extends [1],[2], and unifies them with the results from the literature. In addition, a number of results from the literature are extended to the case c > 1.

  14. Interactive decoding for the CCSDS recommendation for image data compression

    Science.gov (United States)

    García-Vílchez, Fernando; Serra-Sagristà, Joan; Zabala, Alaitz; Pons, Xavier

    2007-10-01

    In 2005, the Consultative Committee for Space Data Systems (CCSDS) approved a new Recommendation (CCSDS 122.0-B-1) for Image Data Compression. Our group has designed a new file syntax for the Recommendation. The proposal consists of adding embedded headers. Such modification provides scalability by quality, spatial location, resolution and component. The main advantages of our proposal are: 1) the definition of multiple types of progression order, which enhances abilities in transmission scenarios, and 2) the support for the extraction and decoding of specific windows of interest without needing to decode the complete code-stream. In this paper we evaluate the performance of our proposal. First we measure the impact of the embedded headers in the encoded stream. Second we compare the compression performance of our technique to JPEG2000.

  15. HDL Implementation of Low Density Parity Check (LDPC Decoder

    Directory of Open Access Journals (Sweden)

    Pawandip Kaur

    2012-03-01

    Full Text Available Low-Density Parity-Check (LDPC codes are one of the most promising error-correcting codes approaching Shannon capacity and have been adopted in many applications. These codes offer huge advantages in terms of coding gain, throughput and power dissipation. Error correction algorithms are often implemented in hardware for fast processing to meet the real-time needs of communication systems. However hardwareimplementation of LDPC decoders using traditional Hardware Description Language (HDL based approach is a complex and time consuming task. In this paper HDL Implementation of Low Density Parity Check Decoder architecture is presented with different rates i.e. 1/2, 2/3, 3/4, 4/7, 8/9, 9/10 and variable data lengths i.e. 8, 16, 32, 64, 128, 256 bits and consequent changeable precision factor.

  16. Video watermarking with empirical PCA-based decoding.

    Science.gov (United States)

    Khalilian, Hanieh; Bajic, Ivan V

    2013-12-01

    A new method for video watermarking is presented in this paper. In the proposed method, data are embedded in the LL subband of wavelet coefficients, and decoding is performed based on the comparison among the elements of the first principal component resulting from empirical principal component analysis (PCA). The locations for data embedding are selected such that they offer the most robust PCA-based decoding. Data are inserted in the LL subband in an adaptive manner based on the energy of high frequency subbands and visual saliency. Extensive testing was performed under various types of attacks, such as spatial attacks (uniform and Gaussian noise and median filtering), compression attacks (MPEG-2, H. 263, and H. 264), and temporal attacks (frame repetition, frame averaging, frame swapping, and frame rate conversion). The results show that the proposed method offers improved performance compared with several methods from the literature, especially under additive noise and compression attacks.

  17. Two-Bit Bit Flipping Decoding of LDPC Codes

    CERN Document Server

    Nguyen, Dung Viet; Marcellin, Michael W

    2011-01-01

    In this paper, we propose a new class of bit flipping algorithms for low-density parity-check (LDPC) codes over the binary symmetric channel (BSC). Compared to the regular (parallel or serial) bit flipping algorithms, the proposed algorithms employ one additional bit at a variable node to represent its "strength." The introduction of this additional bit increases the guaranteed error correction capability by a factor of at least 2. An additional bit can also be employed at a check node to capture information which is beneficial to decoding. A framework for failure analysis of the proposed algorithms is described. These algorithms outperform the Gallager A/B algorithm and the min-sum algorithm at much lower complexity. Concatenation of two-bit bit flipping algorithms show a potential to approach the performance of belief propagation (BP) decoding in the error floor region, also at lower complexity.

  18. Design of LOG-MAP / MAX-LOG-MAP Decoder

    Directory of Open Access Journals (Sweden)

    Mihai TIMIS, PhD Candidate, Dipl.Eng.

    2007-01-01

    Full Text Available The process of turbo-code decoding starts with the formation of a posteriori probabilities (APPs for each data bit, which is followed by choosing the data-bit value that corresponds to the maximum a posteriori (MAP probability for that data bit. Upon reception of a corrupted code-bit sequence, the process of decision making with APPs allows the MAP algorithm to determine the most likely information bit to have been transmitted at each bit time.

  19. Coset decomposition method for storing and decoding fingerprint data

    OpenAIRE

    Mohamed Sayed

    2014-01-01

    Biometrics such as fingerprints, irises, faces, voice, gait and hands are often used for access control, authentication and encryption instead of PIN and passwords. In this paper a syndrome decoding technique is proposed to provide a secure means of storing and matching various biometrics data. We apply an algebraic coding technique called coset decomposition to the model of fingerprint biometrics. The algorithm which reveals the matching between registered and probe fingerprints is modeled a...

  20. Context adaptive binary arithmetic decoding on transport triggered architectures

    Science.gov (United States)

    Rouvinen, Joona; Jääskeläinen, Pekka; Rintaluoma, Tero; Silvén, Olli; Takala, Jarmo

    2008-02-01

    Video coding standards, such as MPEG-4, H.264, and VC1, define hybrid transform based block motion compensated techniques that employ almost the same coding tools. This observation has been a foundation for defining the MPEG Reconfigurable Multimedia Coding framework that targets to facilitate multi-format codec design. The idea is to send a description of the codec with the bit stream, and to reconfigure the coding tools accordingly on-the-fly. This kind of approach favors software solutions, and is a substantial challenge for the implementers of mobile multimedia devices that aim at high energy efficiency. In particularly as high definition formats are about to be required from mobile multimedia devices, variable length decoders are becoming a serious bottleneck. Even at current moderate mobile video bitrates software based variable length decoders swallow a major portion of the resources of a mobile processor. In this paper we present a Transport Triggered Architecture (TTA) based programmable implementation for Context Adaptive Binary Arithmetic de-Coding (CABAC) that is used e.g. in the main profile of H.264 and in JPEG2000. The solution can be used even for other variable length codes.

  1. Efficient Network for Non-Binary QC-LDPC Decoder

    CERN Document Server

    Zhang, Chuan

    2011-01-01

    This paper presents approaches to develop efficient network for non-binary quasi-cyclic LDPC (QC-LDPC) decoders. By exploiting the intrinsic shifting and symmetry properties of the check matrices, significant reduction of memory size and routing complexity can be achieved. Two different efficient network architectures for Class-I and Class-II non-binary QC-LDPC decoders have been proposed, respectively. Comparison results have shown that for the code of the 64-ary (1260, 630) rate-0.5 Class-I code, the proposed scheme can save more than 70.6% hardware required by shuffle network than the state-of-the-art designs. The proposed decoder example for the 32-ary (992, 496) rate-0.5 Class-II code can achieve a 93.8% shuffle network reduction compared with the conventional ones. Meanwhile, based on the similarity of Class-I and Class-II codes, similar shuffle network is further developed to incorporate both classes of codes at a very low cost.

  2. LDPC Decoding for Signal Dependent Visible Light Communication Channels

    Institute of Scientific and Technical Information of China (English)

    YUAN Ming; SHA Xiaoshi; LIANG Xiao; JIANG Ming; WANG Jiaheng; ZHAO Chunming

    2016-01-01

    Avalanche photodiodes (APD) are widely employed in visible light communication (VLC) systems. The general signal dependent Gaussian channel is investigated. Experiment results reveal that symbols on different constellation points under official illumi⁃nance inevitably suffer from different levels of noise due to the multiplication process of APDs. In such a case, conventional log likely⁃hood ratio (LLR) calculation for signal independent channels may cause performance loss. The optimal LLR calculation for decoder is then derived because of the existence of non⁃ignorable APD shot noise. To find the decoding thresholds of the optimal and suboptimal detection schemes, the extrinsic information transfer (EXIT) chat is further analyzed. Finally a modified minimum sum algorithm is suggested with reduced complexity and acceptable performance loss. Numerical simulations show that, with a reg⁃ular (3, 6) low⁃density parity check (LDPC) code of block length 20,000, 0.7 dB gain is achieved with our proposed scheme over the LDPC decoder designed for signal independent noise. It is also found that the coding performance is improved for a larger modulation depth.

  3. The basis of orientation decoding in human primary visual cortex: fine- or coarse-scale biases?

    Science.gov (United States)

    Maloney, Ryan T

    2015-01-01

    Orientation signals in human primary visual cortex (V1) can be reliably decoded from the multivariate pattern of activity as measured with functional magnetic resonance imaging (fMRI). The precise underlying source of these decoded signals (whether by orientation biases at a fine or coarse scale in cortex) remains a matter of some controversy, however. Freeman and colleagues (J Neurosci 33: 19695-19703, 2013) recently showed that the accuracy of decoding of spiral patterns in V1 can be predicted by a voxel's preferred spatial position (the population receptive field) and its coarse orientation preference, suggesting that coarse-scale biases are sufficient for orientation decoding. Whether they are also necessary for decoding remains an open question, and one with implications for the broader interpretation of multivariate decoding results in fMRI studies. Copyright © 2015 the American Physiological Society.

  4. Elimination of the Background Noise of the Decoded Image in Fresnel Zone Plate Scanning Holography

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A method of digitally high pass filtering in frequency domain is proposed to eliminate the background noise of the decoded image in Fresnel zone plate scanning holography. The high pass filter is designed as a circular stop, which should be suitable to suppressing the background noise significantly and remain much low frequency information of the object. The principle of high pass filtering is that the Fourier transform of the decoded image is multiplied with the high pass filter. Thus the frequency spectrum of the decoded image without the background noise is achieved. By inverse Fourier transform of the spectrum of the decoded image after multiplying operation, the decoded image without the background noise is obtained. Both of the computer simulations and the experimental results show that the contrast and the signal-to-noise ratio of the decoded image are significantly improved with digital filtering.

  5. Design and Implementation of Single Chip WCDMA High Speed Channel Decoder

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A memory and driving clock efficient design scheme to achieve WCDMA high-speed channel decoder on a single XILINX' XVC1000E FPGA chip is presented. Using a modified MAP algorithm, say parallel Sliding Window logarithmic Maximum A Posterior (PSW-log-MAP), the on-chip turbo decoder can decode an information bit by only an average of two clocks per iteration. On the other hand, a high-parallel pipeline Viterbi algorithm is adopted to realize the 256-state convolutional code decoding. The final decoder with an 8×chip-clock (30.72MHz) driving can concurrently process a data rate up to 2.5Mbps of turbo coded sequences and a data rate over 400kbps of convolutional codes. There is no extern memory needed. Test results show that the decoding performance is only 0.2~0.3dB or less lost comparing to float simulation.

  6. Serial Min-max Decoding Algorithm Based on Variable Weighting for Nonbinary LDPC Codes

    Directory of Open Access Journals (Sweden)

    Zhongxun Wang

    2013-09-01

    Full Text Available In this paper, we perform an analysis on the min-max decoding algorithm for nonbinary LDPC(low-density parity-check codes and propose serial min-max decoding algorithm. Combining with the weighted processing of the variable node message, we propose serial min-max decoding algorithm based on variable weighting for nonbinary LDPC codes in the end. The simulation indicates that when the bit error rate is 10^-3,compared with serial min-max decoding algorithm ,traditional min-max decoding algorithm and traditional minsum algorithm ,serial min-max decoding algorithm based on variable weighting can offer additional coding gain 0.2dB、0.8dB and 1.4dB respectively in additional white Gaussian noise channel and under binary phase shift keying modulation.  

  7. On the Properties of Neural Machine Translation: Encoder-Decoder Approaches

    OpenAIRE

    Cho, Kyunghyun; van Merrienboer, Bart; Bahdanau, Dzmitry; Bengio, Yoshua

    2014-01-01

    Neural machine translation is a relatively new approach to statistical machine translation based purely on neural networks. The neural machine translation models often consist of an encoder and a decoder. The encoder extracts a fixed-length representation from a variable-length input sentence, and the decoder generates a correct translation from this representation. In this paper, we focus on analyzing the properties of the neural machine translation using two models; RNN Encoder--Decoder and...

  8. Coding/decoding two-dimensional images with orbital angular momentum of light.

    Science.gov (United States)

    Chu, Jiaqi; Li, Xuefeng; Smithwick, Quinn; Chu, Daping

    2016-04-01

    We investigate encoding and decoding of two-dimensional information using the orbital angular momentum (OAM) of light. Spiral phase plates and phase-only spatial light modulators are used in encoding and decoding of OAM states, respectively. We show that off-axis points and spatial variables encoded with a given OAM state can be recovered through decoding with the corresponding complimentary OAM state.

  9. Inter-domain interactions of TDP-43 as decoded by NMR.

    Science.gov (United States)

    Wei, Yuanyuan; Lim, Liangzhong; Wang, Lu; Song, Jianxing

    2016-04-29

    TDP-43 inclusions have been found in ∼97% ALS as well as an increasing spectrum of other neurodegenerative diseases including Alzheimer's. TDP-43 contains an ubiquitin-like fold, two RRMs and a prion-like domain, but whether they interact with each other remains unknown due to being intrinsically aggregation-prone. Nevertheless, this knowledge is pivotal to understanding physiological functions and pathological roles of TDP-43. Here as facilitated by our previous discovery which allowed NMR characterization of TDP-43 and its five dissected fragments, we successfully decoded that TDP-43 does have dynamic inter-domain interactions, which are coordinated by the intrinsically-disordered prion-like domain. Thus, TDP-43 appears to undergo conformational exchanges between "closed" and "open" states which are needed for its functions. Our study thus offers a mechanism by which cellular processes might control TDP-43 physiology and proteinopathy by mediating its inter-domain interactions. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Evaluation of combinatorial cis-regulatory elements for stable gene expression in chicken cells

    Directory of Open Access Journals (Sweden)

    Seo Hee W

    2010-09-01

    Full Text Available Abstract Background Recent successes in biotechnological application of birds are based on their unique physiological traits such as unlimited manipulability onto developing embryos and simple protein constituents of the eggs. However it is not likely that target protein is produced as kinetically expected because various factors affect target gene expression. Although there have been various attempts to minimize the silencing of transgenes, a generalized study that uses multiple cis-acting elements in chicken has not been made. The aim of the present study was to analyze whether various cis-acting elements can help to sustain transgene expression in chicken fibroblasts. Results We investigated the optimal transcriptional regulatory elements for enhancing stable transgene expression in chicken cells. We generated eight constructs that encode enhanced green fluorescent protein (eGFP driven by either CMV or CAG promoters (including the control, containing three types of key regulatory elements: a chicken lysozyme matrix attachment region (cMAR, 5'-DNase I-hypersensitive sites 4 (cHS4, and the woodchuck hepatitis virus posttranscriptional regulatory element (WPRE. Then we transformed immortalized chicken embryonic fibroblasts with these constructs by electroporation, and after cells were expanded under G418 selection, analyzed mRNA levels and mean fluorescence intensity (MFI by quantitative real-time PCR and flow cytometry, respectively. We found that the copy number of each construct significantly decreased as the size of the construct increased (R2 = 0.701. A significant model effect was found in the expression level among various constructs in both mRNA and protein (P cis-acting elements decreased the level of gene silencing as well as the coefficient of variance of eGFP-expressing cells (P Conclusions Our current data show that an optimal combination of cis-acting elements and promoters/enhancers for sustaining gene expression in chicken cells is suggested. These results provide important information for avian transgenesis and gene function studies in poultry.

  11. On the mechanistic nature of epistasis in a canonical cis-regulatory element

    OpenAIRE

    Lagator, Mato; Paix?o, Tiago; Barton, Nicholas H; Bollback, Jonathan P.; Guet, C?lin C.

    2017-01-01

    eLife digest Mutations are changes to DNA that provide the raw material upon which evolution can act. Therefore, to understand evolution, we need to know the effects of mutations, and how those mutations interact with each other (a phenomenon referred to as epistasis). So far, few mathematical models allow scientists to predict the effects of mutations, and even fewer are able to predict epistasis. Biological systems are complex and consist of many proteins and other molecules. Genes are the ...

  12. Mapping cis-Regulatory Domains in the Human Genome UsingMulti-Species Conservation of Synteny

    Energy Technology Data Exchange (ETDEWEB)

    Ahituv, Nadav; Prabhakar, Shyam; Poulin, Francis; Rubin, EdwardM.; Couronne, Olivier

    2005-06-13

    Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle is the large genomic space surrounding targeted genes in which such elements could potentially reside. In order to delineate gene regulatory boundaries we used whole-genome human-mouse-chicken (HMC) and human-mouse-frog (HMF) multiple alignments to compile conserved blocks of synteny (CBS), under the hypothesis that these blocks have been kept intact throughout evolution at least in part by the requirement of regulatory elements to stay linked to the genes that they regulate. A total of 2,116 and 1,942 CBS>200 kb were assembled for HMC and HMF respectively, encompassing 1.53 and 0.86 Gb of human sequence. To support the existence of complex long-range regulatory domains within these CBS we analyzed the prevalence and distribution of chromosomal aberrations leading to position effects (disruption of a genes regulatory environment), observing a clear bias not only for mapping onto CBS but also for longer CBS size. Our results provide a genome wide data set characterizing the regulatory domains of genes and the conserved regulatory elements within them.

  13. Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.

    Science.gov (United States)

    Cubillos, Francisco A; Stegle, Oliver; Grondin, Cécile; Canut, Matthieu; Tisné, Sébastien; Gy, Isabelle; Loudet, Olivier

    2014-11-01

    cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis-acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments.

  14. Extensive cis-Regulatory Variation Robust to Environmental Perturbation in Arabidopsis[W

    Science.gov (United States)

    Cubillos, Francisco A.; Stegle, Oliver; Grondin, Cécile; Canut, Matthieu; Tisné, Sébastien; Gy, Isabelle

    2014-01-01

    cis- and trans-acting factors affect gene expression and responses to environmental conditions. However, for most plant systems, we lack a comprehensive map of these factors and their interaction with environmental variation. Here, we examined allele-specific expression (ASE) in an F1 hybrid to study how alleles from two Arabidopsis thaliana accessions affect gene expression. To investigate the effect of the environment, we used drought stress and developed a variance component model to estimate the combined genetic contributions of cis- and trans-regulatory polymorphisms, environmental factors, and their interactions. We quantified ASE for 11,003 genes, identifying 3318 genes with consistent ASE in control and stress conditions, demonstrating that cis-acting genetic effects are essentially robust to changes in the environment. Moreover, we found 1618 genes with genotype x environment (GxE) interactions, mostly cis x E interactions with magnitude changes in ASE. We found fewer trans x E interactions, but these effects were relatively less robust across conditions, showing more changes in the direction of the effect between environments; this confirms that trans-regulation plays an important role in the response to environmental conditions. Our data provide a detailed map of cis- and trans-regulation and GxE interactions in A. thaliana, laying the ground for mechanistic investigations and studies in other plants and environments. PMID:25428981

  15. Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4

    OpenAIRE

    Hanikenne, Marc; Talke, Ina N.; Haydon, Michael J.; Lanz, Christa; Nolte, Andrea; Motte, Patrick; Kroymann, Juergen; Weigel, Detlef; Krämer, Ute

    2008-01-01

    Little is known about the types of mutations underlying the evolution of species-specific traits. The metal hyperaccumulator Arabidopsis halleri has the rare ability to colonize heavy-metal-polluted soils, and, as an extremophile sister species of Arabidopsis thaliana, it is a powerful model for research on adaptation. A. halleri naturally accumulates and tolerates leaf concentrations as high as 2.2% zinc and 0.28% cadmium in dry biomass. On the basis of transcriptomics studies, metal hyperac...

  16. Cis-regulatory underpinnings of human GLI3 expression in embryonic craniofacial structures and internal organs.

    Science.gov (United States)

    Abbasi, Amir A; Minhas, Rashid; Schmidt, Ansgar; Koch, Sabine; Grzeschik, Karl-Heinz

    2013-10-01

    The zinc finger transcription factor Gli3 is an important mediator of Sonic hedgehog (Shh) signaling. During early embryonic development Gli3 participates in patterning and growth of the central nervous system, face, skeleton, limb, tooth and gut. Precise regulation of the temporal and spatial expression of Gli3 is crucial for the proper specification of these structures in mammals and other vertebrates. Previously we reported a set of human intronic cis-regulators controlling almost the entire known repertoire of endogenous Gli3 expression in mouse neural tube and limbs. However, the genetic underpinning of GLI3 expression in other embryonic domains such as craniofacial structures and internal organs remain elusive. Here we demonstrate in a transgenic mice assay the potential of a subset of human/fish conserved non-coding sequences (CNEs) residing within GLI3 intronic intervals to induce reporter gene expression at known regions of endogenous Gli3 transcription in embryonic domains other than central nervous system (CNS) and limbs. Highly specific reporter expression was observed in craniofacial structures, eye, gut, and genitourinary system. Moreover, the comparison of expression patterns directed by these intronic cis-acting regulatory elements in mouse and zebrafish embryos suggests that in accordance with sequence conservation, the target site specificity of a subset of these elements remains preserved among these two lineages. Taken together with our recent investigations, it is proposed here that during vertebrate evolution the Gli3 expression control acquired multiple, independently acting, intronic enhancers for spatiotemporal patterning of CNS, limbs, craniofacial structures and internal organs.

  17. Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models

    DEFF Research Database (Denmark)

    Wong, Wendy S W; Nielsen, Rasmus

    2007-01-01

    of the increasing availability of comparative genomic data. RESULTS: We develop a method for finding regulatory modules in Eukaryotic species using phylogenetic data. Using computer simulations and analysis of real data, we show that the use of phylogenetic hidden Markov model can lead to an increase in accuracy...

  18. New cis-regulatory elements in the Rht-D1b locus region of wheat

    Science.gov (United States)

    Fifteen gene-containing BACs with accumulated length of 1.82-Mb from the Rht-D1b locus region weresequenced and compared in detail with the orthologous regions of rice, sorghum, and maize. Our results show that Rht-D1b represents a conserved genomic region as implied by high gene sequence identity...

  19. Subfunctionalization of duplicated zebrafish pax6 genes by cis-regulatory divergence

    National Research Council Canada - National Science Library

    Kleinjan, Dirk A; Bancewicz, Ruth M; Gautier, Philippe; Dahm, Ralf; Schonthaler, Helia B; Damante, Giuseppe; Seawright, Anne; Hever, Ann M; Yeyati, Patricia L; van Heyningen, Veronica; Coutinho, Pedro

    2008-01-01

    Gene duplication is a major driver of evolutionary divergence. In most vertebrates a single PAX6 gene encodes a transcription factor required for eye, brain, olfactory system, and pancreas development...

  20. Interactions between glucocorticoid treatment and cis-regulatory polymorphisms contribute to cellular response phenotypes.

    Directory of Open Access Journals (Sweden)

    Joseph C Maranville

    2011-07-01

    Full Text Available Glucocorticoids (GCs mediate physiological responses to environmental stress and are commonly used as pharmaceuticals. GCs act primarily through the GC receptor (GR, a transcription factor. Despite their clear biomedical importance, little is known about the genetic architecture of variation in GC response. Here we provide an initial assessment of variability in the cellular response to GC treatment by profiling gene expression and protein secretion in 114 EBV-transformed B lymphocytes of African and European ancestry. We found that genetic variation affects the response of nearby genes and exhibits distinctive patterns of genotype-treatment interactions, with genotypic effects evident in either only GC-treated or only control-treated conditions. Using a novel statistical framework, we identified interactions that influence the expression of 26 genes known to play central roles in GC-related pathways (e.g. NQO1, AIRE, and SGK1 and that influence the secretion of IL6.

  1. Systematic identification of cis-regulatory sequences active in mouse and human embryonic stem cells.

    Directory of Open Access Journals (Sweden)

    Marica Grskovic

    2007-08-01

    Full Text Available Understanding the transcriptional regulation of pluripotent cells is of fundamental interest and will greatly inform efforts aimed at directing differentiation of embryonic stem (ES cells or reprogramming somatic cells. We first analyzed the transcriptional profiles of mouse ES cells and primordial germ cells and identified genes upregulated in pluripotent cells both in vitro and in vivo. These genes are enriched for roles in transcription, chromatin remodeling, cell cycle, and DNA repair. We developed a novel computational algorithm, CompMoby, which combines analyses of sequences both aligned and non-aligned between different genomes with a probabilistic segmentation model to systematically predict short DNA motifs that regulate gene expression. CompMoby was used to identify conserved overrepresented motifs in genes upregulated in pluripotent cells. We show that the motifs are preferentially active in undifferentiated mouse ES and embryonic germ cells in a sequence-specific manner, and that they can act as enhancers in the context of an endogenous promoter. Importantly, the activity of the motifs is conserved in human ES cells. We further show that the transcription factor NF-Y specifically binds to one of the motifs, is differentially expressed during ES cell differentiation, and is required for ES cell proliferation. This study provides novel insights into the transcriptional regulatory networks of pluripotent cells. Our results suggest that this systematic approach can be broadly applied to understanding transcriptional networks in mammalian species.

  2. Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity

    Science.gov (United States)

    Gaiti, Federico; Jindrich, Katia; Fernandez-Valverde, Selene L; Roper, Kathrein E; Degnan, Bernard M; Tanurdžić, Miloš

    2017-01-01

    Combinatorial patterns of histone modifications regulate developmental and cell type-specific gene expression and underpin animal complexity, but it is unclear when this regulatory system evolved. By analysing histone modifications in a morphologically-simple, early branching animal, the sponge Amphimedonqueenslandica, we show that the regulatory landscape used by complex bilaterians was already in place at the dawn of animal multicellularity. This includes distal enhancers, repressive chromatin and transcriptional units marked by H3K4me3 that vary with levels of developmental regulation. Strikingly, Amphimedon enhancers are enriched in metazoan-specific microsyntenic units, suggesting that their genomic location is extremely ancient and likely to place constraints on the evolution of surrounding genes. These results suggest that the regulatory foundation for spatiotemporal gene expression evolved prior to the divergence of sponges and eumetazoans, and was necessary for the evolution of animal multicellularity. DOI: http://dx.doi.org/10.7554/eLife.22194.001 PMID:28395144

  3. Complete Decoding and Reporting of Aviation Routine Weather Reports (METARs)

    Science.gov (United States)

    Lui, Man-Cheung Max

    2014-01-01

    Aviation Routine Weather Report (METAR) provides surface weather information at and around observation stations, including airport terminals. These weather observations are used by pilots for flight planning and by air traffic service providers for managing departure and arrival flights. The METARs are also an important source of weather data for Air Traffic Management (ATM) analysts and researchers at NASA and elsewhere. These researchers use METAR to correlate severe weather events with local or national air traffic actions that restrict air traffic, as one example. A METAR is made up of multiple groups of coded text, each with a specific standard coding format. These groups of coded text are located in two sections of a report: Body and Remarks. The coded text groups in a U.S. METAR are intended to follow the coding standards set by National Oceanic and Atmospheric Administration (NOAA). However, manual data entry and edits made by a human report observer may result in coded text elements that do not follow the standards, especially in the Remarks section. And contrary to the standards, some significant weather observations are noted only in the Remarks section and not in the Body section of the reports. While human readers can infer the intended meaning of non-standard coding of weather conditions, doing so with a computer program is far more challenging. However such programmatic pre-processing is necessary to enable efficient and faster database query when researchers need to perform any significant historical weather analysis. Therefore, to support such analysis, a computer algorithm was developed to identify groups of coded text anywhere in a report and to perform subsequent decoding in software. The algorithm considers common deviations from the standards and data entry mistakes made by observers. The implemented software code was tested to decode 12 million reports and the decoding process was able to completely interpret 99.93 of the reports. This

  4. Computational drug discovery

    Institute of Scientific and Technical Information of China (English)

    Si-sheng OU-YANG; Jun-yan LU; Xiang-qian KONG; Zhong-jie LIANG; Cheng LUO; Hualiang JIANG

    2012-01-01

    Computational drug discovery is an effective strategy for accelerating and economizing drug discovery and development process.Because of the dramatic increase in the availability of biological macromolecule and small molecule information,the applicability of computational drug discovery has been extended and broadly applied to nearly every stage in the drug discovery and development workflow,including target identification and validation,lead discovery and optimization and preclinical tests.Over the past decades,computational drug discovery methods such as molecular docking,pharmacophore modeling and mapping,de novo design,molecular similarity calculation and sequence-based virtual screening have been greatly improved.In this review,we present an overview of these important computational methods,platforms and successful applications in this field.

  5. VLSI design of turbo decoder for integrated communication system on a chip applications

    Science.gov (United States)

    Fang, Wai-Chi; Sethuram, Ashwin; Belevi, Kemal

    2003-01-01

    A high-throughput low-power turbo decoder core has been developed for integrated communication system applications such as satellite communications, wireless LAN, digital TV, cable modem, Digital Video Broadcast (DVB), and xDSL systems. The turbo decoder is based on convolutional constituent codes, which outperform all other Forward Error Correction techniques. This turbo decoder core is parameterizable and can be modified easily to fit any size for advanced communication system-on-chip products. The turbo decoder core provides Forward Error Correction of up to 15 Mbits/sec on a 0.13-micron CMOS FPGA prototyping chip at a power of 0.1 watts.

  6. VLSI Architectures for Sliding-Window-Based Space-Time Turbo Trellis Code Decoders

    Directory of Open Access Journals (Sweden)

    Georgios Passas

    2012-01-01

    Full Text Available The VLSI implementation of SISO-MAP decoders used for traditional iterative turbo coding has been investigated in the literature. In this paper, a complete architectural model of a space-time turbo code receiver that includes elementary decoders is presented. These architectures are based on newly proposed building blocks such as a recursive add-compare-select-offset (ACSO unit, A-, B-, Γ-, and LLR output calculation modules. Measurements of complexity and decoding delay of several sliding-window-technique-based MAP decoder architectures and a proposed parameter set lead to defining equations and comparison between those architectures.

  7. Analysis of Iterated Hard Decision Decoding of Product Codes with Reed-Solomon Component Codes

    DEFF Research Database (Denmark)

    Justesen, Jørn; Høholdt, Tom

    2007-01-01

    Products of Reed-Solomon codes are important in applications because they offer a combination of large blocks, low decoding complexity, and good performance. A recent result on random graphs can be used to show that with high probability a large number of errors can be corrected by iterating...... minimum distance decoding. We present an analysis related to density evolution which gives the exact asymptotic value of the decoding threshold and also provides a closed form approximation to the distribution of errors in each step of the decoding of finite length codes....

  8. Decoding skills in children with language impairment: contributions of phonological processing and classroom experiences.

    Science.gov (United States)

    Tambyraja, Sherine R; Farquharson, Kelly; Logan, Jessica A R; Justice, Laura M

    2015-05-01

    Children with language impairment (LI) often demonstrate difficulties with word decoding. Research suggests that child-level (i.e., phonological processing) and environmental-level (i.e., classroom quality) factors both contribute to decoding skills in typically developing children. The present study examined the extent to which these same factors influence the decoding skills of children with LI, and the extent to which classroom quality moderates the relationship between phonological processing and decoding. Kindergarten and first-grade children with LI (n = 198) were assessed on measures of phonological processing and decoding twice throughout the academic year. Live classroom observations were conducted to assess classroom quality with respect to emotional support and instructional support. Hierarchical regression analyses revealed that of the 3 phonological processing variables included, only phonological awareness significantly predicted spring decoding outcomes when controlling for children's age and previous decoding ability. One aspect of classroom quality (emotional support) was also predictive of decoding, but there was no significant interaction between classroom quality and phonological processing. This study provides further evidence that phonological awareness is an important skill to assess in children with LI and that high-quality classroom environments can be positively associated with children's decoding outcomes.

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

    Directory of Open Access Journals (Sweden)

    Ahmed Azouaoui

    2012-09-01

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

  10. Sensitivity analysis of the channel estimation deviation to the MAP decoding algorithm

    Institute of Scientific and Technical Information of China (English)

    WAN Ke; FAN Ping-zhi

    2006-01-01

    As a necessary input parameter for maximum a-posteriori(MAP) decoding algorithm,SNR is normally obtained from the channel estimation unit.Corresponding research indicated that SNR estimation deviation degraded the performance of Turbo decoding significantly.In this paper,MAP decoding algorithm with SNR estimation deviation was investigated in detail,and the degradation mechanism of Turbo decoding was explained analytically.The theoretical analysis and computer simulation disclosed the specific reasons for the performance degradation when SNR estimation was less than the actual value,and for the higher sensitivity of SNR estimation to long-frame Turbo codes.

  11. On the Joint Error-and-Erasure Decoding for Irreducible Polynomial Remainder Codes

    CERN Document Server

    Yu, Jiun-Hung

    2012-01-01

    A general class of polynomial remainder codes is considered. Such codes are very flexible in rate and length and include Reed-Solomon codes as a special case. As an extension of previous work, two joint error-and-erasure decoding approaches are proposed. In particular, both the decoding approaches by means of a fixed transform are treated in a way compatible with the error-only decoding. In the end, a collection of gcd-based decoding algorithm is obtained, some of which appear to be new even when specialized to Reed-Solomon codes.

  12. Analysis and design of raptor codes for joint decoding using Information Content evolution

    CERN Document Server

    Venkiah, Auguste; Declercq, David

    2007-01-01

    In this paper, we present an analytical analysis of the convergence of raptor codes under joint decoding over the binary input additive white noise channel (BIAWGNC), and derive an optimization method. We use Information Content evolution under Gaussian approximation, and focus on a new decoding scheme that proves to be more efficient: the joint decoding of the two code components of the raptor code. In our general model, the classical tandem decoding scheme appears to be a subcase, and thus, the design of LT codes is also possible.

  13. Continuous motion decoding from EMG using independent component analysis and adaptive model training.

    Science.gov (United States)

    Zhang, Qin; Xiong, Caihua; Chen, Wenbin

    2014-01-01

    Surface Electromyography (EMG) is popularly used to decode human motion intention for robot movement control. Traditional motion decoding method uses pattern recognition to provide binary control command which can only move the robot as predefined limited patterns. In this work, we proposed a motion decoding method which can accurately estimate 3-dimensional (3-D) continuous upper limb motion only from multi-channel EMG signals. In order to prevent the muscle activities from motion artifacts and muscle crosstalk which especially obviously exist in upper limb motion, the independent component analysis (ICA) was applied to extract the independent source EMG signals. The motion data was also transferred from 4-manifold to 2-manifold by the principle component analysis (PCA). A hidden Markov model (HMM) was proposed to decode the motion from the EMG signals after the model trained by an adaptive model identification process. Experimental data were used to train the decoding model and validate the motion decoding performance. By comparing the decoded motion with the measured motion, it is found that the proposed motion decoding strategy was feasible to decode 3-D continuous motion from EMG signals.

  14. Reliable knowledge discovery

    CERN Document Server

    Dai, Honghua; Smirnov, Evgueni

    2012-01-01

    Reliable Knowledge Discovery focuses on theory, methods, and techniques for RKDD, a new sub-field of KDD. It studies the theory and methods to assure the reliability and trustworthiness of discovered knowledge and to maintain the stability and consistency of knowledge discovery processes. RKDD has a broad spectrum of applications, especially in critical domains like medicine, finance, and military. Reliable Knowledge Discovery also presents methods and techniques for designing robust knowledge-discovery processes. Approaches to assessing the reliability of the discovered knowledge are introduc

  15. An Improved Unscented Kalman Filter Based Decoder for Cortical Brain-Machine Interfaces

    Science.gov (United States)

    Li, Simin; Li, Jie; Li, Zheng

    2016-01-01

    Brain-machine interfaces (BMIs) seek to connect brains with machines or computers directly, for application in areas such as prosthesis control. For this application, the accuracy of the decoding of movement intentions is crucial. We aim to improve accuracy by designing a better encoding model of primary motor cortical activity during hand movements and combining this with decoder engineering refinements, resulting in a new unscented Kalman filter based decoder, UKF2, which improves upon our previous unscented Kalman filter decoder, UKF1. The new encoding model includes novel acceleration magnitude, position-velocity interaction, and target-cursor-distance features (the decoder does not require target position as input, it is decoded). We add a novel probabilistic velocity threshold to better determine the user's intent to move. We combine these improvements with several other refinements suggested by others in the field. Data from two Rhesus monkeys indicate that the UKF2 generates offline reconstructions of hand movements (mean CC 0.851) significantly more accurately than the UKF1 (0.833) and the popular position-velocity Kalman filter (0.812). The encoding model of the UKF2 could predict the instantaneous firing rate of neurons (mean CC 0.210), given kinematic variables and past spiking, better than the encoding models of these two decoders (UKF1: 0.138, p-v Kalman: 0.098). In closed-loop experiments where each monkey controlled a computer cursor with each decoder in turn, the UKF2 facilitated faster task completion (mean 1.56 s vs. 2.05 s) and higher Fitts's Law bit rate (mean 0.738 bit/s vs. 0.584 bit/s) than the UKF1. These results suggest that the modeling and decoder engineering refinements of the UKF2 improve decoding performance. We believe they can be used to enhance other decoders as well. PMID:28066170

  16. An Improved Unscented Kalman Filter Based Decoder for Cortical Brain-Machine Interfaces.

    Science.gov (United States)

    Li, Simin; Li, Jie; Li, Zheng

    2016-01-01

    Brain-machine interfaces (BMIs) seek to connect brains with machines or computers directly, for application in areas such as prosthesis control. For this application, the accuracy of the decoding of movement intentions is crucial. We aim to improve accuracy by designing a better encoding model of primary motor cortical activity during hand movements and combining this with decoder engineering refinements, resulting in a new unscented Kalman filter based decoder, UKF2, which improves upon our previous unscented Kalman filter decoder, UKF1. The new encoding model includes novel acceleration magnitude, position-velocity interaction, and target-cursor-distance features (the decoder does not require target position as input, it is decoded). We add a novel probabilistic velocity threshold to better determine the user's intent to move. We combine these improvements with several other refinements suggested by others in the field. Data from two Rhesus monkeys indicate that the UKF2 generates offline reconstructions of hand movements (mean CC 0.851) significantly more accurately than the UKF1 (0.833) and the popular position-velocity Kalman filter (0.812). The encoding model of the UKF2 could predict the instantaneous firing rate of neurons (mean CC 0.210), given kinematic variables and past spiking, better than the encoding models of these two decoders (UKF1: 0.138, p-v Kalman: 0.098). In closed-loop experiments where each monkey controlled a computer cursor with each decoder in turn, the UKF2 facilitated faster task completion (mean 1.56 s vs. 2.05 s) and higher Fitts's Law bit rate (mean 0.738 bit/s vs. 0.584 bit/s) than the UKF1. These results suggest that the modeling and decoder engineering refinements of the UKF2 improve decoding performance. We believe they can be used to enhance other decoders as well.

  17. Academic Drug Discovery Centres

    DEFF Research Database (Denmark)

    Kirkegaard, Henriette Schultz; Valentin, Finn

    2014-01-01

    Academic drug discovery centres (ADDCs) are seen as one of the solutions to fill the innovation gap in early drug discovery, which has proven challenging for previous organisational models. Prior studies of ADDCs have identified the need to analyse them from the angle of their economic...... their performance....

  18. Higgs Discovery Movie

    CERN Multimedia

    2014-01-01

    The ATLAS & CMS Experiments Celebrate the 2nd Anniversary of the Discovery of the Higgs boson. Here, are some images of the path from LHC startup to Nobel Prize, featuring a musical composition by Roger Zare, performed by the Donald Sinta Quartet, called “LHC”. Happy Discovery Day!

  19. Friends' Discovery Camp

    Science.gov (United States)

    Seymour, Seth

    2008-01-01

    This article features Friends' Discovery Camp, a program that allows children with and without autism spectrum disorder to learn and play together. In Friends' Discovery Camp, campers take part in sensory-rich experiences, ranging from hands-on activities and performing arts to science experiments and stories teaching social skills. Now in its 7th…

  20. Serendipity and Scientific Discovery.

    Science.gov (United States)

    Rosenman, Martin F.

    1988-01-01

    The discovery of penicillin is cited in a discussion of the role of serendipity as it relates to scientific discovery. The importance of sagacity as a personality trait is noted. Successful researchers have questioning minds, are willing to view data from several perspectives, and recognize and appreciate the unexpected. (JW)

  1. Empirical Discovery in Linguistics

    CERN Document Server

    Pericliev, V

    1995-01-01

    A discovery system for detecting correspondences in data is described, based on the familiar induction methods of J. S. Mill. Given a set of observations, the system induces the ``causally'' related facts in these observations. Its application to empirical linguistic discovery is described.

  2. Service discovery at home

    NARCIS (Netherlands)

    Sundramoorthy, V.; Scholten, Johan; Jansen, P.G.; Hartel, Pieter H.

    2003-01-01

    Service discovery is a fairly new field that kicked off since the advent of ubiquitous computing and has been found essential in the making of intelligent networks by implementing automated discovery and remote control between devices. This paper provides an overview and comparison of several promin

  3. Service Discovery At Home

    NARCIS (Netherlands)

    Sundramoorthy, V.; Scholten, Johan; Jansen, P.G.; Hartel, Pieter H.

    2003-01-01

    Service discovery is a fady new field that kicked off since the advent of ubiquitous computing and has been found essential in the making of intelligent networks by implementing automated discovery and remote control between deviies. This paper provides an ovewiew and comparison of several prominent

  4. Service discovery at home

    NARCIS (Netherlands)

    Sundramoorthy, V.; Scholten, Johan; Jansen, P.G.; Hartel, Pieter H.

    2003-01-01

    Service discovery is a fairly new field that kicked off since the advent of ubiquitous computing and has been found essential in the making of intelligent networks by implementing automated discovery and remote control between devices. This paper provides an overview and comparison of several

  5. Service Discovery At Home

    NARCIS (Netherlands)

    Sundramoorthy, V.; Scholten, Johan; Jansen, P.G.; Hartel, Pieter H.

    Service discovery is a fady new field that kicked off since the advent of ubiquitous computing and has been found essential in the making of intelligent networks by implementing automated discovery and remote control between deviies. This paper provides an ovewiew and comparison of several prominent

  6. Service discovery at home

    NARCIS (Netherlands)

    Sundramoorthy, Vasughi; Scholten, Hans; Jansen, Pierre; Hartel, Pieter

    2003-01-01

    Service discovery is a fairly new field that kicked off since the advent of ubiquitous computing and has been found essential in the making of intelligent networks by implementing automated discovery and remote control between devices. This paper provides an overview and comparison of several promin

  7. "Eureka, Eureka!" Discoveries in Science

    Science.gov (United States)

    Agarwal, Pankaj

    2011-01-01

    Accidental discoveries have been of significant value in the progress of science. Although accidental discoveries are more common in pharmacology and chemistry, other branches of science have also benefited from such discoveries. While most discoveries are the result of persistent research, famous accidental discoveries provide a fascinating…

  8. Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes

    Science.gov (United States)

    Lin, Shu

    1998-01-01

    A code trellis is a graphical representation of a code, block or convolutional, in which every path represents a codeword (or a code sequence for a convolutional code). This representation makes it possible to implement Maximum Likelihood Decoding (MLD) of a code with reduced decoding complexity. The most well known trellis-based MLD algorithm is the Viterbi algorithm. The trellis representation was first introduced and used for convolutional codes [23]. This representation, together with the Viterbi decoding algorithm, has resulted in a wide range of applications of convolutional codes for error control in digital communications over the last two decades. There are two major reasons for this inactive period of research in this area. First, most coding theorists at that time believed that block codes did not have simple trellis structure like convolutional codes and maximum likelihood decoding of linear block codes using the Viterbi algorithm was practically impossible, except for very short block codes. Second, since almost all of the linear block codes are constructed algebraically or based on finite geometries, it was the belief of many coding theorists that algebraic decoding was the only way to decode these codes. These two reasons seriously hindered the development of efficient soft-decision decoding methods for linear block codes and their applications to error control in digital communications. This led to a general belief that block codes are inferior to convolutional codes and hence, that they were not useful. Chapter 2 gives a brief review of linear block codes. The goal is to provide the essential background material for the development of trellis structure and trellis-based decoding algorithms for linear block codes in the later chapters. Chapters 3 through 6 present the fundamental concepts, finite-state machine model, state space formulation, basic structural properties, state labeling, construction procedures, complexity, minimality, and

  9. Central Decoding for Multiple Description Codes based on Domain Partitioning

    Directory of Open Access Journals (Sweden)

    M. Spiertz

    2006-01-01

    Full Text Available Multiple Description Codes (MDC can be used to trade redundancy against packet loss resistance for transmitting data over lossy diversity networks. In this work we focus on MD transform coding based on domain partitioning. Compared to Vaishampayan’s quantizer based MDC, domain based MD coding is a simple approach for generating different descriptions, by using different quantizers for each description. Commonly, only the highest rate quantizer is used for reconstruction. In this paper we investigate the benefit of using the lower rate quantizers to enhance the reconstruction quality at decoder side. The comparison is done on artificial source data and on image data. 

  10. Research on coding and decoding method for digital levels.

    Science.gov (United States)

    Tu, Li-fen; Zhong, Si-dong

    2011-01-20

    A new coding and decoding method for digital levels is proposed. It is based on an area-array CCD sensor and adopts mixed coding technology. By taking advantage of redundant information in a digital image signal, the contradiction that the field of view and image resolution restrict each other in a digital level measurement is overcome, and the geodetic leveling becomes easier. The experimental results demonstrate that the uncertainty of measurement is 1 mm when the measuring range is between 2 m and 100 m, which can meet practical needs.

  11. Design of 4:16 decoder using reversible logic gates

    Directory of Open Access Journals (Sweden)

    Santhi Chebiyyam

    2016-04-01

    Full Text Available Reversible logic has received great importance in the recent years because of its feature of reduction in power dissipation. It finds application in low power digital designs, quantum computing, nanotechnology, DNA computing etc. Large number of researches are currently ongoing on sequential and combinational circuits using reversible logic. Decoders are one of the most important circuits used in combinational logic. Different approaches have been proposed for their design. In this article, we have proposed a novel design of 4:16.

  12. Polynomial system solving for decoding linear codes and algebraic cryptanalysis

    OpenAIRE

    2009-01-01

    This thesis is devoted to applying symbolic methods to the problems of decoding linear codes and of algebraic cryptanalysis. The paradigm we employ here is as follows. We reformulate the initial problem in terms of systems of polynomial equations over a finite field. The solution(s) of such systems should yield a way to solve the initial problem. Our main tools for handling polynomials and polynomial systems in such a paradigm is the technique of Gröbner bases and normal form reductions. The ...

  13. A New Simple Ultrahigh Speed Decoding Algorithm for BCH Code

    Institute of Scientific and Technical Information of China (English)

    唐建军; 纪越峰

    2002-01-01

    In order to content with forward error correction (FEC) technology of the high-speed optical communication system, a new simple decoding algorithm for triple-error correcting Bose, Chaudhuri, and Hocquenghem (BCH) code is proposed. Without complicated matrix-operation or division-operation or intricate iterative algorithm, the algorithm is high efficient and high-speed because of its simplicity in structure. The result of hardware emulation confirms that the algorithm is feasible completely. Introduction of the parallel structure increases the speed of coding greatly. The algorithm can be used in the high-speed optical communication system and other fields.

  14. Joint Source-Channel Decoding Scheme for Image Transmission over Wireless Channel

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    We improve the iterative decoding algorithm by utilizing the "leaked" residual redundancy at the output of the source encoder without changing the encoder structure for the noisy channel.The experimental results show that using the residual redundancy of the compressed source in channel decoding is an effective method to improve the error correction performance.

  15. The Euclidean Algorithm for Generalized Minimum Distance Decoding of Reed-Solomon Codes

    CERN Document Server

    Kampf, Sabine

    2010-01-01

    This paper presents a method to merge Generalized Minimum Distance decoding of Reed-Solomon codes with the extended Euclidean algorithm. By merge, we mean that the steps taken to perform the Generalized Minimum Distance decoding are similar to those performed by the extended Euclidean algorithm. The resulting algorithm has a complexity of O(n^2).

  16. Decoding Ability in French as a Foreign Language and Language Learning Motivation

    Science.gov (United States)

    Erler, Lynn; Macaro, Ernesto

    2011-01-01

    This study examined the relationships between decoding ability (the ability to relate graphemes to phonemes) in French as a foreign language, self-reported use of such decoding, and dimensions of motivation, specifically self-efficacy and attribution, among young-beginner learners in England. It investigated whether these factors were related to a…

  17. Multi-Trial Guruswami–Sudan Decoding for Generalised Reed–Solomon Codes

    DEFF Research Database (Denmark)

    Nielsen, Johan Sebastian Rosenkilde; Zeh, Alexander

    2013-01-01

    An iterated refinement procedure for the Guruswami–Sudan list decoding algorithm for Generalised Reed–Solomon codes based on Alekhnovich’s module minimisation is proposed. The method is parametrisable and allows variants of the usual list decoding approach. In particular, finding the list...

  18. The Three Stages of Coding and Decoding in Listening Courses of College Japanese Specialty

    Science.gov (United States)

    Yang, Fang

    2008-01-01

    The main focus of research papers on listening teaching published in recent years is the theoretical meanings of decoding on the training of listening comprehension ability. Although in many research papers the bottom-up approach and top-down approach, information processing mode theory, are applied to illustrate decoding and to emphasize the…

  19. A Parallel Decoding Algorithm for Short Polar Codes Based on Error Checking and Correcting

    Science.gov (United States)

    Pan, Xiaofei; Pan, Kegang; Ye, Zhan; Gong, Chao

    2014-01-01

    We propose a parallel decoding algorithm based on error checking and correcting to improve the performance of the short polar codes. In order to enhance the error-correcting capacity of the decoding algorithm, we first derive the error-checking equations generated on the basis of the frozen nodes, and then we introduce the method to check the errors in the input nodes of the decoder by the solutions of these equations. In order to further correct those checked errors, we adopt the method of modifying the probability messages of the error nodes with constant values according to the maximization principle. Due to the existence of multiple solutions of the error-checking equations, we formulate a CRC-aided optimization problem of finding the optimal solution with three different target functions, so as to improve the accuracy of error checking. Besides, in order to increase the throughput of decoding, we use a parallel method based on the decoding tree to calculate probability messages of all the nodes in the decoder. Numerical results show that the proposed decoding algorithm achieves better performance than that of some existing decoding algorithms with the same code length. PMID:25540813

  20. Iterative channel decoding of FEC-based multiple-description codes.

    Science.gov (United States)

    Chang, Seok-Ho; Cosman, Pamela C; Milstein, Laurence B

    2012-03-01

    Multiple description coding has been receiving attention as a robust transmission framework for multimedia services. This paper studies the iterative decoding of FEC-based multiple description codes. The proposed decoding algorithms take advantage of the error detection capability of Reed-Solomon (RS) erasure codes. The information of correctly decoded RS codewords is exploited to enhance the error correction capability of the Viterbi algorithm at the next iteration of decoding. In the proposed algorithm, an intradescription interleaver is synergistically combined with the iterative decoder. The interleaver does not affect the performance of noniterative decoding but greatly enhances the performance when the system is iteratively decoded. We also address the optimal allocation of RS parity symbols for unequal error protection. For the optimal allocation in iterative decoding, we derive mathematical equations from which the probability distributions of description erasures can be generated in a simple way. The performance of the algorithm is evaluated over an orthogonal frequency-division multiplexing system. The results show that the performance of the multiple description codes is significantly enhanced.