BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.
De Witte, Dieter; Van de Velde, Jan; Decap, Dries; Van Bel, Michiel; Audenaert, Pieter; Demeester, Piet; Dhoedt, Bart; Vandepoele, Klaas; Fostier, Jan
2015-12-01
The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species. Existing methods for comparative motif discovery usually rely on pregenerated multiple sequence alignments, which are difficult to obtain for more diverged species such as plants. As a consequence, misaligned regulatory elements often remain undetected. We present a novel algorithm that supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and screened for conservation using the branch length score. Additionally, a confidence score is established in a genome-wide fashion. In order to take advantage of a cloud computing infrastructure, the MapReduce programming model is adopted. The method is applied to four monocotyledon plant species and it is shown that high-scoring motifs are significantly enriched for open chromatin regions in Oryza sativa and for transcription factor binding sites inferred through protein-binding microarrays in O.sativa and Zea mays. Furthermore, the method is shown to recover experimentally profiled ga2ox1-like KN1 binding sites in Z.mays. BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.
A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis
Energy Technology Data Exchange (ETDEWEB)
Keys, David N.; Lee, Byung-in; Di Gregorio, Anna; Harafuji, Naoe; Detter, Chris; Wang, Mei; Kahsai, Orsalem; Ahn, Sylvia; Arellano, Andre; Zhang, Quin; Trong, Stephan; Doyle, Sharon A.; Satoh, Noriyuki; Satou, Yutaka; Saiga, Hidetoshi; Christian, Allen; Rokhsar, Dan; Hawkins, Trevor L.; Levine, Mike; Richardson, Paul
2005-01-05
A screen for the systematic identification of cis-regulatory elements within large (>100 kb) genomic domains containing Hox genes was performed by using the basal chordate Ciona intestinalis. Randomly generated DNA fragments from bacterial artificial chromosomes containing two clusters of Hox genes were inserted into a vector upstream of a minimal promoter and lacZ reporter gene. A total of 222 resultant fusion genes were separately electroporated into fertilized eggs, and their regulatory activities were monitored in larvae. In sum, 21 separable cis-regulatory elements were found. These include eight Hox linked domains that drive expression in nested anterior-posterior domains of ectodermally derived tissues. In addition to vertebrate-like CNS regulation, the discovery of cis-regulatory domains that drive epidermal transcription suggests that C. intestinalis has arthropod-like Hox patterning in the epidermis.
A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model
Directory of Open Access Journals (Sweden)
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.
A New Algorithm for Identifying Cis-Regulatory Modules Based on Hidden Markov Model
2017-01-01
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. PMID:28497059
Statistical significance of cis-regulatory modules
Directory of Open Access Journals (Sweden)
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.
In silico discovery of transcription regulatory elements in Plasmodium falciparum
Directory of Open Access Journals (Sweden)
Le Roch Karine G
2008-02-01
Full Text Available Abstract Background With the sequence of the Plasmodium falciparum genome and several global mRNA and protein life cycle expression profiling projects now completed, elucidating the underlying networks of transcriptional control important for the progression of the parasite life cycle is highly pertinent to the development of new anti-malarials. To date, relatively little is known regarding the specific mechanisms the parasite employs to regulate gene expression at the mRNA level, with studies of the P. falciparum genome sequence having revealed few cis-regulatory elements and associated transcription factors. Although it is possible the parasite may evoke mechanisms of transcriptional control drastically different from those used by other eukaryotic organisms, the extreme AT-rich nature of P. falciparum intergenic regions (~90% AT presents significant challenges to in silico cis-regulatory element discovery. Results We have developed an algorithm called Gene Enrichment Motif Searching (GEMS that uses a hypergeometric-based scoring function and a position-weight matrix optimization routine to identify with high-confidence regulatory elements in the nucleotide-biased and repeat sequence-rich P. falciparum genome. When applied to promoter regions of genes contained within 21 co-expression gene clusters generated from P. falciparum life cycle microarray data using the semi-supervised clustering algorithm Ontology-based Pattern Identification, GEMS identified 34 putative cis-regulatory elements associated with a variety of parasite processes including sexual development, cell invasion, antigenic variation and protein biosynthesis. Among these candidates were novel motifs, as well as many of the elements for which biological experimental evidence already exists in the Plasmodium literature. To provide evidence for the biological relevance of a cell invasion-related element predicted by GEMS, reporter gene and electrophoretic mobility shift assays
Evolution of Cis-Regulatory Elements and Regulatory Networks in Duplicated Genes of Arabidopsis.
Arsovski, Andrej A; Pradinuk, Julian; Guo, Xu Qiu; Wang, Sishuo; Adams, Keith L
2015-12-01
Plant genomes contain large numbers of duplicated genes that contribute to the evolution of new functions. Following duplication, genes can exhibit divergence in their coding sequence and their expression patterns. Changes in the cis-regulatory element landscape can result in changes in gene expression patterns. High-throughput methods developed recently can identify potential cis-regulatory elements on a genome-wide scale. Here, we use a recent comprehensive data set of DNase I sequencing-identified cis-regulatory binding sites (footprints) at single-base-pair resolution to compare binding sites and network connectivity in duplicated gene pairs in Arabidopsis (Arabidopsis thaliana). We found that duplicated gene pairs vary greatly in their cis-regulatory element architecture, resulting in changes in regulatory network connectivity. Whole-genome duplicates (WGDs) have approximately twice as many footprints in their promoters left by potential regulatory proteins than do tandem duplicates (TDs). The WGDs have a greater average number of footprint differences between paralogs than TDs. The footprints, in turn, result in more regulatory network connections between WGDs and other genes, forming denser, more complex regulatory networks than shown by TDs. When comparing regulatory connections between duplicates, WGDs had more pairs in which the two genes are either partially or fully diverged in their network connections, but fewer genes with no network connections than the TDs. There is evidence of younger TDs and WGDs having fewer unique connections compared with older duplicates. This study provides insights into cis-regulatory element evolution and network divergence in duplicated genes. © 2015 American Society of Plant Biologists. All Rights Reserved.
Gene set-based module discovery in the breast cancer transcriptome
Directory of Open Access Journals (Sweden)
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.
Jiménez-Delgado, Senda; Pascual-Anaya, Juan; Garcia-Fernàndez, Jordi
2009-07-01
The discovery that most regulatory genes were conserved among animals from distant phyla challenged the ideas that gene duplication and divergence of homologous coding sequences were the basis for major morphological changes in metazoan evolution. In recent years, however, the interest for the roles, conservation and changes of non-coding sequences grew-up in parallel with genome sequencing projects. Presently, many independent studies are highlighting the importance that subtle changes in cis-regulatory regions had in the evolution of morphology trough the Animal Kingdom. Here we will show and discuss some of these studies, and underscore the future of cis-Evo-Devo research. Nevertheless, we would also explore how gene duplication, which includes duplication of regulatory regions, may have been critical for spatial or temporal co-option of new regulatory networks, causing the deployment of new transcriptome scenarios, and how these induced morphological changes were critical for the evolution of new forms. Forty years after Susumu Ohno famous sentence 'natural selection merely modifies, while redundancy creates', we suggest the alternative: 'natural selection modifies, while redundancy of cis-regulatory elements innovates', and propose the Duplication-Degeneration-Innovation model to explain the increased evolvability of duplicated cis-regulatory regions. Paradoxically, making regulation simpler by subfunctionalization paved the path for future complexity or, in other words, 'to make it simple to make it complex'.
Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.
Directory of Open Access Journals (Sweden)
Jongmin Nam
Full Text Available Cis-regulatory DNA sequences causally mediate patterns of gene expression, but efficient experimental analysis of these control systems has remained challenging. Here we develop a new version of "barcoded" DNA-tag reporters, "Nanotags" that permit simultaneous quantitative analysis of up to 130 distinct cis-regulatory modules (CRMs. The activities of these reporters are measured in single experiments by the NanoString RNA counting method and other quantitative procedures. We demonstrate the efficiency of the Nanotag method by simultaneously measuring hourly temporal activities of 126 CRMs from 46 genes in the developing sea urchin embryo, otherwise a virtually impossible task. Nanotags are also used in gene perturbation experiments to reveal cis-regulatory responses of many CRMs at once. Nanotag methodology can be applied to many research areas, ranging from gene regulatory networks to functional and evolutionary genomics.
On the Concept of Cis-regulatory Information: From Sequence Motifs to Logic Functions
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.
Cis-regulatory somatic mutations and gene-expression alteration in B-cell lymphomas.
Mathelier, Anthony; Lefebvre, Calvin; Zhang, Allen W; Arenillas, David J; Ding, Jiarui; Wasserman, Wyeth W; Shah, Sohrab P
2015-04-23
With the rapid increase of whole-genome sequencing of human cancers, an important opportunity to analyze and characterize somatic mutations lying within cis-regulatory regions has emerged. A focus on protein-coding regions to identify nonsense or missense mutations disruptive to protein structure and/or function has led to important insights; however, the impact on gene expression of mutations lying within cis-regulatory regions remains under-explored. We analyzed somatic mutations from 84 matched tumor-normal whole genomes from B-cell lymphomas with accompanying gene expression measurements to elucidate the extent to which these cancers are disrupted by cis-regulatory mutations. We characterize mutations overlapping a high quality set of well-annotated transcription factor binding sites (TFBSs), covering a similar portion of the genome as protein-coding exons. Our results indicate that cis-regulatory mutations overlapping predicted TFBSs are enriched in promoter regions of genes involved in apoptosis or growth/proliferation. By integrating gene expression data with mutation data, our computational approach culminates with identification of cis-regulatory mutations most likely to participate in dysregulation of the gene expression program. The impact can be measured along with protein-coding mutations to highlight key mutations disrupting gene expression and pathways in cancer. Our study yields specific genes with disrupted expression triggered by genomic mutations in either the coding or the regulatory space. It implies that mutated regulatory components of the genome contribute substantially to cancer pathways. Our analyses demonstrate that identifying genomically altered cis-regulatory elements coupled with analysis of gene expression data will augment biological interpretation of mutational landscapes of cancers.
Yang, Tzu-Hsien; Wang, Chung-Ching; Hung, Po-Cheng; Wu, Wei-Sheng
2014-01-01
Cis-regulatory modules (CRMs), or the DNA sequences required for regulating gene expression, play the central role in biological researches on transcriptional regulation in metazoan species. Nowadays, the systematic understanding of CRMs still mainly resorts to computational methods due to the time-consuming and small-scale nature of experimental methods. But the accuracy and reliability of different CRM prediction tools are still unclear. Without comparative cross-analysis of the results and combinatorial consideration with extra experimental information, there is no easy way to assess the confidence of the predicted CRMs. This limits the genome-wide understanding of CRMs. It is known that transcription factor binding and epigenetic profiles tend to determine functions of CRMs in gene transcriptional regulation. Thus integration of the genome-wide epigenetic profiles with systematically predicted CRMs can greatly help researchers evaluate and decipher the prediction confidence and possible transcriptional regulatory functions of these potential CRMs. However, these data are still fragmentary in the literatures. Here we performed the computational genome-wide screening for potential CRMs using different prediction tools and constructed the pioneer database, cisMEP (cis-regulatory module epigenetic profile database), to integrate these computationally identified CRMs with genomic epigenetic profile data. cisMEP collects the literature-curated TFBS location data and nine genres of epigenetic data for assessing the confidence of these potential CRMs and deciphering the possible CRM functionality. cisMEP aims to provide a user-friendly interface for researchers to assess the confidence of different potential CRMs and to understand the functions of CRMs through experimentally-identified epigenetic profiles. The deposited potential CRMs and experimental epigenetic profiles for confidence assessment provide experimentally testable hypotheses for the molecular mechanisms
Pathogenic adaptation of intracellular bacteria by rewiring a cis-regulatory input function.
Osborne, Suzanne E; Walthers, Don; Tomljenovic, Ana M; Mulder, David T; Silphaduang, Uma; Duong, Nancy; Lowden, Michael J; Wickham, Mark E; Waller, Ross F; Kenney, Linda J; Coombes, Brian K
2009-03-10
The acquisition of DNA by horizontal gene transfer enables bacteria to adapt to previously unexploited ecological niches. Although horizontal gene transfer and mutation of protein-coding sequences are well-recognized forms of pathogen evolution, the evolutionary significance of cis-regulatory mutations in creating phenotypic diversity through altered transcriptional outputs is not known. We show the significance of regulatory mutation for pathogen evolution by mapping and then rewiring a cis-regulatory module controlling a gene required for murine typhoid. Acquisition of a binding site for the Salmonella pathogenicity island-2 regulator, SsrB, enabled the srfN gene, ancestral to the Salmonella genus, to play a role in pathoadaptation of S. typhimurium to a host animal. We identified the evolved cis-regulatory module and quantified the fitness gain that this regulatory output accrues for the bacterium using competitive infections of host animals. Our findings highlight a mechanism of pathogen evolution involving regulatory mutation that is selected because of the fitness advantage the new regulatory output provides the incipient clones.
Ibraheem, Omodele; Botha, Christiaan E J; Bradley, Graeme
2010-12-01
The regulation of gene expression involves a multifarious regulatory system. Each gene contains a unique combination of cis-acting regulatory sequence elements in the 5' regulatory region that determines its temporal and spatial expression. Cis-acting regulatory elements are essential transcriptional gene regulatory units; they control many biological processes and stress responses. Thus a full understanding of the transcriptional gene regulation system will depend on successful functional analyses of cis-acting elements. Cis-acting regulatory elements present within the 5' regulatory region of the sucrose transporter gene families in rice (Oryza sativa Japonica cultivar-group) and Arabidopsis thaliana, were identified using a bioinformatics approach. The possible cis-acting regulatory elements were predicted by scanning 1.5kbp of 5' regulatory regions of the sucrose transporter genes translational start sites, using Plant CARE, PLACE and Genomatix Matinspector professional databases. Several cis-acting regulatory elements that are associated with plant development, plant hormonal regulation and stress response were identified, and were present in varying frequencies within the 1.5kbp of 5' regulatory region, among which are; A-box, RY, CAT, Pyrimidine-box, Sucrose-box, ABRE, ARF, ERE, GARE, Me-JA, ARE, DRE, GA-motif, GATA, GT-1, MYC, MYB, W-box, and I-box. This result reveals the probable cis-acting regulatory elements that possibly are involved in the expression and regulation of sucrose transporter gene families in rice and Arabidopsis thaliana during cellular development or environmental stress conditions. Copyright © 2010 Elsevier Ltd. All rights reserved.
Genome-wide prediction of cis-regulatory regions using supervised deep learning methods.
Li, Yifeng; Shi, Wenqiang; Wasserman, Wyeth W
2018-05-31
In the human genome, 98% of DNA sequences are non-protein-coding regions that were previously disregarded as junk DNA. In fact, non-coding regions host a variety of cis-regulatory regions which precisely control the expression of genes. Thus, Identifying active cis-regulatory regions in the human genome is critical for understanding gene regulation and assessing the impact of genetic variation on phenotype. The developments of high-throughput sequencing and machine learning technologies make it possible to predict cis-regulatory regions genome wide. Based on rich data resources such as the Encyclopedia of DNA Elements (ENCODE) and the Functional Annotation of the Mammalian Genome (FANTOM) projects, we introduce DECRES based on supervised deep learning approaches for the identification of enhancer and promoter regions in the human genome. Due to their ability to discover patterns in large and complex data, the introduction of deep learning methods enables a significant advance in our knowledge of the genomic locations of cis-regulatory regions. Using models for well-characterized cell lines, we identify key experimental features that contribute to the predictive performance. Applying DECRES, we delineate locations of 300,000 candidate enhancers genome wide (6.8% of the genome, of which 40,000 are supported by bidirectional transcription data), and 26,000 candidate promoters (0.6% of the genome). The predicted annotations of cis-regulatory regions will provide broad utility for genome interpretation from functional genomics to clinical applications. The DECRES model demonstrates potentials of deep learning technologies when combined with high-throughput sequencing data, and inspires the development of other advanced neural network models for further improvement of genome annotations.
Creating and validating cis-regulatory maps of tissue-specific gene expression regulation
O'Connor, Timothy R.; Bailey, Timothy L.
2014-01-01
Predicting which genomic regions control the transcription of a given gene is a challenge. We present a novel computational approach for creating and validating maps that associate genomic regions (cis-regulatory modules–CRMs) with genes. The method infers regulatory relationships that explain gene expression observed in a test tissue using widely available genomic data for ‘other’ tissues. To predict the regulatory targets of a CRM, we use cross-tissue correlation between histone modifications present at the CRM and expression at genes within 1 Mbp of it. To validate cis-regulatory maps, we show that they yield more accurate models of gene expression than carefully constructed control maps. These gene expression models predict observed gene expression from transcription factor binding in the CRMs linked to that gene. We show that our maps are able to identify long-range regulatory interactions and improve substantially over maps linking genes and CRMs based on either the control maps or a ‘nearest neighbor’ heuristic. Our results also show that it is essential to include CRMs predicted in multiple tissues during map-building, that H3K27ac is the most informative histone modification, and that CAGE is the most informative measure of gene expression for creating cis-regulatory maps. PMID:25200088
Organization of cis-acting regulatory elements in osmotic- and cold-stress-responsive promoters.
Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo
2005-02-01
cis-Acting regulatory elements are important molecular switches involved in the transcriptional regulation of a dynamic network of gene activities controlling various biological processes, including abiotic stress responses, hormone responses and developmental processes. In particular, understanding regulatory gene networks in stress response cascades depends on successful functional analyses of cis-acting elements. The ever-improving accuracy of transcriptome expression profiling has led to the identification of various combinations of cis-acting elements in the promoter regions of stress-inducible genes involved in stress and hormone responses. Here we discuss major cis-acting elements, such as the ABA-responsive element (ABRE) and the dehydration-responsive element/C-repeat (DRE/CRT), that are a vital part of ABA-dependent and ABA-independent gene expression in osmotic and cold stress responses.
Kwon, Andrew T.; Chou, Alice Yi; Arenillas, David J.; Wasserman, Wyeth W.
2011-01-01
We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs) using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene expression to differentiated C2C12 myotubes. A subset of 19 CRMs validated as functional in the assay. The rate of predictive success reveals striking limitations of computational regulatory sequence analysis methods for CRM discovery. Motif-based methods performed no better than predictions based only on sequence conservation. Analysis of the properties of the functional sequences relative to inactive sequences identifies nucleotide sequence composition can be an important characteristic to incorporate in future methods for improved predictive specificity. Muscle-related TFBSs predicted within the functional sequences display greater sequence conservation than non-TFBS flanking regions. Comparison with recent MyoD and histone modification ChIP-Seq data supports the validity of the functional regions. PMID:22144875
Directory of Open Access Journals (Sweden)
Andrew T Kwon
2011-12-01
Full Text Available We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene expression to differentiated C2C12 myotubes. A subset of 19 CRMs validated as functional in the assay. The rate of predictive success reveals striking limitations of computational regulatory sequence analysis methods for CRM discovery. Motif-based methods performed no better than predictions based only on sequence conservation. Analysis of the properties of the functional sequences relative to inactive sequences identifies nucleotide sequence composition can be an important characteristic to incorporate in future methods for improved predictive specificity. Muscle-related TFBSs predicted within the functional sequences display greater sequence conservation than non-TFBS flanking regions. Comparison with recent MyoD and histone modification ChIP-Seq data supports the validity of the functional regions.
Leyfer, Dmitriy; Weng, Zhiping
2005-09-01
A holistic approach to the study of cellular processes is identifying both gene-expression changes and regulatory elements promoting such changes. Cellular regulatory processes can be viewed as transcriptional modules (TMs), groups of coexpressed genes regulated by groups of transcription factors (TFs). We set out to devise a method that would identify TMs while avoiding arbitrary thresholds on TM sizes and number. Assuming that gene expression is determined by TFs that bind to the gene's promoter, clustering of genes based on TF binding sites (cis-elements) should create gene groups similar to those obtained by gene expression clustering. Intersections between the expression and cis-element-based gene clusters reveal TMs. Statistical significance assigned to each TM allows identification of regulatory units of any size. Our method correctly identifies the number and sizes of TMs on simulated datasets. We demonstrate that yeast experimental TMs are biologically relevant by comparing them with MIPS and GO categories. Our modules are in statistically significant agreement with TMs from other research groups. This work suggests that there is no preferential division of biological processes into regulatory units; each degree of partitioning exhibits a slice of biological network revealing hierarchical modular organization of transcriptional regulation.
Directory of Open Access Journals (Sweden)
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.
A method for selecting cis-acting regulatory sequences that respond to small molecule effectors
Directory of Open Access Journals (Sweden)
Allas Ülar
2010-08-01
Full Text Available Abstract Background Several cis-acting regulatory sequences functioning at the level of mRNA or nascent peptide and specifically influencing transcription or translation have been described. These regulatory elements often respond to specific chemicals. Results We have developed a method that allows us to select cis-acting regulatory sequences that respond to diverse chemicals. The method is based on the β-lactamase gene containing a random sequence inserted into the beginning of the ORF. Several rounds of selection are used to isolate sequences that suppress β-lactamase expression in response to the compound under study. We have isolated sequences that respond to erythromycin, troleandomycin, chloramphenicol, meta-toluate and homoserine lactone. By introducing synonymous and non-synonymous mutations we have shown that at least in the case of erythromycin the sequences act at the peptide level. We have also tested the cross-activities of the constructs and found that in most cases the sequences respond most strongly to the compound on which they were isolated. Conclusions Several selected peptides showed ligand-specific changes in amino acid frequencies, but no consensus motif could be identified. This is consistent with previous observations on natural cis-acting peptides, showing that it is often impossible to demonstrate a consensus. Applying the currently developed method on a larger scale, by selecting and comparing an extended set of sequences, might allow the sequence rules underlying the activity of cis-acting regulatory peptides to be identified.
Directory of Open Access Journals (Sweden)
Gizem Kalay
2010-11-01
Full Text Available cis-regulatory DNA sequences known as enhancers control gene expression in space and time. They are central to metazoan development and are often responsible for changes in gene regulation that contribute to phenotypic evolution. Here, we examine the sequence, function, and genomic location of enhancers controlling tissue- and cell-type specific expression of the yellow gene in six Drosophila species. yellow is required for the production of dark pigment, and its expression has evolved largely in concert with divergent pigment patterns. Using Drosophila melanogaster as a transgenic host, we examined the expression of reporter genes in which either 5' intergenic or intronic sequences of yellow from each species controlled the expression of Green Fluorescent Protein. Surprisingly, we found that sequences controlling expression in the wing veins, as well as sequences controlling expression in epidermal cells of the abdomen, thorax, and wing, were located in different genomic regions in different species. By contrast, sequences controlling expression in bristle-associated cells were located in the intron of all species. Differences in the precise pattern of spatial expression within the developing epidermis of D. melanogaster transformants usually correlated with adult pigmentation in the species from which the cis-regulatory sequences were derived, which is consistent with cis-regulatory evolution affecting yellow expression playing a central role in Drosophila pigmentation divergence. Sequence comparisons among species favored a model in which sequential nucleotide substitutions were responsible for the observed changes in cis-regulatory architecture. Taken together, these data demonstrate frequent changes in yellow cis-regulatory architecture among Drosophila species. Similar analyses of other genes, combining in vivo functional tests of enhancer activity with in silico comparative genomics, are needed to determine whether the pattern of
Computational and molecular dissection of an X-box cis-Regulatory module
Warrington, Timothy Burton
2015-01-01
Ciliopathies are a class of human diseases marked by dysfunction of the cellular organelle, cilia. While many of the molecular components that make up cilia have been identified and studied, comparatively little is understood about the transcriptional regulation of genes encoding these components. The conserved transcription factor Regulatory Factor X (RFX)/DAF-19, which acts through binding to the cis-regulatory motif known as X-box, has been shown to regulate ciliary genes in many animals f...
Dynamic SPR monitoring of yeast nuclear protein binding to a cis-regulatory element
International Nuclear Information System (INIS)
Mao, Grace; Brody, James P.
2007-01-01
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 16 bp region of Saccharomyces cerevisiae chromosome 5 onto a gold surface. This 16 bp 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 0.014 s -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
Coevolution within a transcriptional network by compensatory trans and cis mutations
Kuo, D.
2010-10-26
Transcriptional networks have been shown to evolve very rapidly, prompting questions as to how such changes arise and are tolerated. Recent comparisons of transcriptional networks across species have implicated variations in the cis-acting DNA sequences near genes as the main cause of divergence. What is less clear is how these changes interact with trans-acting changes occurring elsewhere in the genetic circuit. Here, we report the discovery of a system of compensatory trans and cis mutations in the yeast AP-1 transcriptional network that allows for conserved transcriptional regulation despite continued genetic change. We pinpoint a single species, the fungal pathogen Candida glabrata, in which a trans mutation has occurred very recently in a single AP-1 family member, distinguishing it from its Saccharomyces ortholog. Comparison of chromatin immunoprecipitation profiles between Candida and Saccharomyces shows that, despite their different DNA-binding domains, the AP-1 orthologs regulate a conserved block of genes. This conservation is enabled by concomitant changes in the cis-regulatory motifs upstream of each gene. Thus, both trans and cis mutations have perturbed the yeast AP-1 regulatory system in such a way as to compensate for one another. This demonstrates an example of “coevolution” between a DNA-binding transcription factor and its cis-regulatory site, reminiscent of the coevolution of protein binding partners.
Decoding the genome with an integrative analysis tool: combinatorial CRM Decoder.
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.
CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors
J.C. Corbo (Joseph); K.A. Lawrence (Karen); M. Karlstetter (Marcus); C.A. Myers (Connie); M. Abdelaziz (Musa); W. Dirkes (William); K. Weigelt (Karin); M. Seifert (Martin); V. Benes (Vladimir); L.G. Fritsche (Lars); B.H.F. Weber (Bernhard); T. Langmann (Thomas)
2010-01-01
textabstractApproximately 98% of mammalian DNA is noncoding, yet we understand relatively little about the function of this enigmatic portion of the genome. The cis-regulatory elements that control gene expression reside in noncoding regions and can be identified by mapping the binding sites of
PlantCARE, a plant cis-acting regulatory element database
Rombauts, Stephane; Déhais, Patrice; Van Montagu, Marc; Rouzé, Pierre
1999-01-01
PlantCARE is a database of plant cis- acting regulatory elements, enhancers and repressors. Besides the transcription motifs found on a sequence, it also offers a link to the EMBL entry that contains the full gene sequence as well as a description of the conditions in which a motif becomes functional. The information on these sites is given by matrices, consensus and individual site sequences on particular genes, depending on the available information. PlantCARE is a relational database avail...
Cis-regulatory elements in the primate brain: from functional specialization to neurodegeneration
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
Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.
Directory of Open Access Journals (Sweden)
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.
Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord.
José-Edwards, Diana S; Oda-Ishii, Izumi; Kugler, Jamie E; Passamaneck, Yale J; Katikala, Lavanya; Nibu, Yutaka; Di Gregorio, Anna
2015-12-01
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.
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.
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
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.
In silico modeling of epigenetic-induced changes in photoreceptor cis-regulatory elements.
Hossain, Reafa A; Dunham, Nicholas R; Enke, Raymond A; Berndsen, Christopher E
2018-01-01
DNA methylation is a well-characterized epigenetic repressor of mRNA transcription in many plant and vertebrate systems. However, the mechanism of this repression is not fully understood. The process of transcription is controlled by proteins that regulate recruitment and activity of RNA polymerase by binding to specific cis-regulatory sequences. Cone-rod homeobox (CRX) is a well-characterized mammalian transcription factor that controls photoreceptor cell-specific gene expression. Although much is known about the functions and DNA binding specificity of CRX, little is known about how DNA methylation modulates CRX binding affinity to genomic cis-regulatory elements. We used bisulfite pyrosequencing of human ocular tissues to measure DNA methylation levels of the regulatory regions of RHO , PDE6B, PAX6 , and LINE1 retrotransposon repeats. To describe the molecular mechanism of repression, we used molecular modeling to illustrate the effect of DNA methylation on human RHO regulatory sequences. In this study, we demonstrate an inverse correlation between DNA methylation in regulatory regions adjacent to the human RHO and PDE6B genes and their subsequent transcription in human ocular tissues. Docking of CRX to the DNA models shows that CRX interacts with the grooves of these sequences, suggesting changes in groove structure could regulate binding. Molecular dynamics simulations of the RHO promoter and enhancer regions show changes in the flexibility and groove width upon epigenetic modification. Models also demonstrate changes in the local dynamics of CRX binding sites within RHO regulatory sequences which may account for the repression of CRX-dependent transcription. Collectively, these data demonstrate epigenetic regulation of CRX binding sites in human retinal tissue and provide insight into the mechanism of this mode of epigenetic regulation to be tested in future experiments.
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
Using hexamers to predict cis-regulatory motifs in Drosophila
Directory of Open Access Journals (Sweden)
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.
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.
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. © 2015. Published by The Company of Biologists Ltd.
Sun, Eric I; Leyn, Semen A; Kazanov, Marat D; Saier, Milton H; Novichkov, Pavel S; Rodionov, Dmitry A
2013-09-02
In silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels.An increasing number of riboswitches and other cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis. A comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs (including thiamin pyrophosphate and cobalamin riboswitches that control the cofactor metabolism) are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations. The reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. The obtained genome
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
Discovery of cis-elements between sorghum and rice using co-expression and evolutionary conservation
Directory of Open Access Journals (Sweden)
Haberer Georg
2009-06-01
Full Text Available Abstract Background The spatiotemporal regulation of gene expression largely depends on the presence and absence of cis-regulatory sites in the promoter. In the economically highly important grass family, our knowledge of transcription factor binding sites and transcriptional networks is still very limited. With the completion of the sorghum genome and the available rice genome sequence, comparative promoter analyses now allow genome-scale detection of conserved cis-elements. Results In this study, we identified thousands of phylogenetic footprints conserved between orthologous rice and sorghum upstream regions that are supported by co-expression information derived from three different rice expression data sets. In a complementary approach, cis-motifs were discovered by their highly conserved co-occurrence in syntenic promoter pairs. Sequence conservation and matches to known plant motifs support our findings. Expression similarities of gene pairs positively correlate with the number of motifs that are shared by gene pairs and corroborate the importance of similar promoter architectures for concerted regulation. This strongly suggests that these motifs function in the regulation of transcript levels in rice and, presumably also in sorghum. Conclusion Our work provides the first large-scale collection of cis-elements for rice and sorghum and can serve as a paradigm for cis-element analysis through comparative genomics in grasses in general.
Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees.
Chabot, Adrien; Shrit, Ralla A; Blekhman, Ran; Gilad, Yoav
2007-08-01
Most phenotypic differences between human and chimpanzee are likely to result from differences in gene regulation, rather than changes to protein-coding regions. To date, however, only a handful of human-chimpanzee nucleotide differences leading to changes in gene regulation have been identified. To hone in on differences in regulatory elements between human and chimpanzee, we focused on 10 genes that were previously found to be differentially expressed between the two species. We then designed reporter gene assays for the putative human and chimpanzee promoters of the 10 genes. Of seven promoters that we found to be active in human liver cell lines, human and chimpanzee promoters had significantly different activity in four cases, three of which recapitulated the gene expression difference seen in the microarray experiment. For these three genes, we were therefore able to demonstrate that a change in cis influences expression differences between humans and chimpanzees. Moreover, using site-directed mutagenesis on one construct, the promoter for the DDA3 gene, we were able to identify three nucleotides that together lead to a cis regulatory difference between the species. High-throughput application of this approach can provide a map of regulatory element differences between humans and our close evolutionary relatives.
Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.
Pierstorff, Nora; Bergman, Casey M; Wiehe, Thomas
2006-12-01
Predicting cis-regulatory modules (CRMs) in higher eukaryotes is a challenging computational task. Commonly used methods to predict CRMs based on the signal of transcription factor binding sites (TFBS) are limited by prior information about transcription factor specificity. More general methods that bypass the reliance on TFBS models are needed for comprehensive CRM prediction. We have developed a method to predict CRMs called CisPlusFinder that identifies high density regions of perfect local ungapped sequences (PLUSs) based on multiple species conservation. By assuming that PLUSs contain core TFBS motifs that are locally overrepresented, the method attempts to capture the expected features of CRM structure and evolution. Applied to a benchmark dataset of CRMs involved in early Drosophila development, CisPlusFinder predicts more annotated CRMs than all other methods tested. Using the REDfly database, we find that some 'false positive' predictions in the benchmark dataset correspond to recently annotated CRMs. Our work demonstrates that CRM prediction methods that combine comparative genomic data with statistical properties of DNA may achieve reasonable performance when applied genome-wide in the absence of an a priori set of known TFBS motifs. The program CisPlusFinder can be downloaded at http://jakob.genetik.uni-koeln.de/bioinformatik/people/nora/nora.html. All software is licensed under the Lesser GNU Public License (LGPL).
Phylogeny based discovery of regulatory elements
Directory of Open Access Journals (Sweden)
Cohen Barak A
2006-05-01
Full Text Available Abstract Background Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advantage of an explicit model for the constrained evolution of functional DNA sequences. Results We developed a probabilistic framework that combines an HKY85 model, which assigns probabilities to different base substitutions between species, and weight matrix models of transcription factor binding sites, which describe the probabilities of observing particular nucleotides at specific positions in the binding site. The method incorporates the phylogenies of the species under consideration and takes into account the position specific variation of transcription factor binding sites. Using our framework we assessed the suitability of alignments of genomic sequences from commonly used species as substrates for comparative genomic approaches to regulatory motif finding. We then applied this technique to Saccharomyces cerevisiae and related species by examining all possible six base pair DNA sequences (hexamers and identifying sequences that are conserved in a significant number of promoters. By combining similar conserved hexamers we reconstructed known cis-regulatory motifs and made predictions of previously unidentified motifs. We tested one prediction experimentally, finding it to be a regulatory element involved in the transcriptional response to glucose. Conclusion The experimental validation of a regulatory element prediction missed by other large-scale motif finding studies demonstrates that our approach is a useful addition to the current suite of tools for finding regulatory motifs.
Yang, Peng; Wu, Min; Guo, Jing; Kwoh, Chee Keong; Przytycka, Teresa M; Zheng, Jie
2014-02-17
As a fundamental genomic element, meiotic recombination hotspot plays important roles in life sciences. Thus uncovering its regulatory mechanisms has broad impact on biomedical research. Despite the recent identification of the zinc finger protein PRDM9 and its 13-mer binding motif as major regulators for meiotic recombination hotspots, other regulators remain to be discovered. Existing methods for finding DNA sequence motifs of recombination hotspots often rely on the enrichment of co-localizations between hotspots and short DNA patterns, which ignore the cross-individual variation of recombination rates and sequence polymorphisms in the population. Our objective in this paper is to capture signals encoded in genetic variations for the discovery of recombination-associated DNA motifs. Recently, an algorithm called "LDsplit" has been designed to detect the association between single nucleotide polymorphisms (SNPs) and proximal meiotic recombination hotspots. The association is measured by the difference of population recombination rates at a hotspot between two alleles of a candidate SNP. Here we present an open source software tool of LDsplit, with integrative data visualization for recombination hotspots and their proximal SNPs. Applying LDsplit on SNPs inside an established 7-mer motif bound by PRDM9 we observed that SNP alleles preserving the original motif tend to have higher recombination rates than the opposite alleles that disrupt the motif. Running on SNP windows around hotspots each containing an occurrence of the 7-mer motif, LDsplit is able to guide the established motif finding algorithm of MEME to recover the 7-mer motif. In contrast, without LDsplit the 7-mer motif could not be identified. LDsplit is a software tool for the discovery of cis-regulatory DNA sequence motifs stimulating meiotic recombination hotspots by screening and narrowing down to hotspot associated SNPs. It is the first computational method that utilizes the genetic variation of
Larson, Nicholas B; McDonnell, Shannon K; Fogarty, Zach; Larson, Melissa C; Cheville, John; Riska, Shaun; Baheti, Saurabh; Weber, Alexandra M; Nair, Asha A; Wang, Liang; O'Brien, Daniel; Davila, Jaime; Schaid, Daniel J; Thibodeau, Stephen N
2017-10-17
Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis -acting associations due to study limitations. While trans -eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans -eQTL associations are mediated by cis -regulated genes, such as transcription factors. Leveraging a data-driven gene co-expression network, we conducted a comprehensive cis -mediator analysis using RNA-Seq data from 471 normal prostate tissue samples to identify downstream regulatory associations of previously identified prostate cancer risk variants. We discovered multiple trans -eQTL associations that were significantly mediated by cis -regulated transcripts, four of which involved risk locus 17q12, proximal transcription factor HNF1B , and target trans -genes with known HNF response elements ( MIA2 , SRC , SEMA6A , KIF12 ). We additionally identified evidence of cis -acting down-regulation of MSMB via rs10993994 corresponding to reduced co-expression of NDRG1 . The majority of these cis -mediator relationships demonstrated trans -eQTL replicability in 87 prostate tissue samples from the Gene-Tissue Expression Project. These findings provide further biological context to known risk loci and outline new hypotheses for investigation into the etiology of prostate cancer.
Bucsenez, M; Rüping, B; Behrens, S; Twyman, R M; Noll, G A; Prüfer, D
2012-09-01
The sieve element occlusion (SEO) gene family includes several members that are expressed specifically in immature sieve elements (SEs) in the developing phloem of dicotyledonous plants. To determine how this restricted expression profile is achieved, we analysed the SE-specific Medicago truncatula SEO-F1 promoter (PMtSEO-F1) by constructing deletion, substitution and hybrid constructs and testing them in transgenic tobacco plants using green fluorescent protein as a reporter. This revealed four promoter regions, each containing cis-regulatory elements that activate transcription in SEs. One of these segments also contained sufficient information to suppress PMtSEO-F1 transcription in the phloem companion cells (CCs). Subsequent in silico analysis revealed several candidate cis-regulatory elements that PMtSEO-F1 shares with other SEO promoters. These putative sieve element boxes (PSE boxes) are promising candidates for cis-regulatory elements controlling the SE-specific expression of PMtSEO-F1. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.
Zhang, Weixiong; Ruan, Jianhua; Ho, Tuan-Hua David; You, Youngsook; Yu, Taotao; Quatrano, Ralph S
2005-07-15
A fundamental problem of computational genomics is identifying the genes that respond to certain endogenous cues and environmental stimuli. This problem can be referred to as targeted gene finding. Since gene regulation is mainly determined by the binding of transcription factors and cis-regulatory DNA sequences, most existing gene annotation methods, which exploit the conservation of open reading frames, are not effective in finding target genes. A viable approach to targeted gene finding is to exploit the cis-regulatory elements that are known to be responsible for the transcription of target genes. Given such cis-elements, putative target genes whose promoters contain the elements can be identified. As a case study, we apply the above approach to predict the genes in model plant Arabidopsis thaliana which are inducible by a phytohormone, abscisic acid (ABA), and abiotic stress, such as drought, cold and salinity. We first construct and analyze two ABA specific cis-elements, ABA-responsive element (ABRE) and its coupling element (CE), in A.thaliana, based on their conservation in rice and other cereal plants. We then use the ABRE-CE module to identify putative ABA-responsive genes in A.thaliana. Based on RT-PCR verification and the results from literature, this method has an accuracy rate of 67.5% for the top 40 predictions. The cis-element based targeted gene finding approach is expected to be widely applicable since a large number of cis-elements in many species are available.
The path from biomarker discovery to regulatory qualification
Goodsaid, Federico
2013-01-01
The Path from Biomarker Discovery to Regulatory Qualification is a unique guide that focuses on biomarker qualification, its history and current regulatory settings in both the US and abroad. This multi-contributed book provides a detailed look at the next step to developing biomarkers for clinical use and covers overall concepts, challenges, strategies and solutions based on the experiences of regulatory authorities and scientists. Members of the regulatory, pharmaceutical and biomarker development communities will benefit the most from using this book-it is a complete and practical guide to biomarker qualification, providing valuable insight to an ever-evolving and important area of regulatory science. For complimentary access to chapter 13, 'Classic' Biomarkers of Liver Injury, by John R. Senior, Associate Director for Science, Food and Drug Administration, Silver Spring, Maryland, USA, please visit the following site: http://tinyurl.com/ClassicBiomarkers Contains a collection of experiences of different...
REDfly: a Regulatory Element Database for Drosophila.
Gallo, Steven M; Li, Long; Hu, Zihua; Halfon, Marc S
2006-02-01
Bioinformatics studies of transcriptional regulation in the metazoa are significantly hindered by the absence of readily available data on large numbers of transcriptional cis-regulatory modules (CRMs). Even the richly annotated Drosophila melanogaster genome lacks extensive CRM information. We therefore present here a database of Drosophila CRMs curated from the literature complete with both DNA sequence and a searchable description of the gene expression pattern regulated by each CRM. This resource should greatly facilitate the development of computational approaches to CRM discovery as well as bioinformatics analyses of regulatory sequence properties and evolution.
Passamaneck, Yale J; Katikala, Lavanya; Perrone, Lorena; Dunn, Matthew P; Oda-Ishii, Izumi; Di Gregorio, Anna
2009-11-01
The notochord is a defining feature of the chordate body plan. Experiments in ascidian, frog and mouse embryos have shown that co-expression of Brachyury and FoxA class transcription factors is required for notochord development. However, studies on the cis-regulatory sequences mediating the synergistic effects of these transcription factors are complicated by the limited knowledge of notochord genes and cis-regulatory modules (CRMs) that are directly targeted by both. We have identified an easily testable model for such investigations in a 155-bp notochord-specific CRM from the ascidian Ciona intestinalis. This CRM contains functional binding sites for both Ciona Brachyury (Ci-Bra) and FoxA (Ci-FoxA-a). By combining point mutation analysis and misexpression experiments, we demonstrate that binding of both transcription factors to this CRM is necessary and sufficient to activate transcription. To gain insights into the cis-regulatory criteria controlling its activity, we investigated the organization of the transcription factor binding sites within the 155-bp CRM. The 155-bp sequence contains two Ci-Bra binding sites with identical core sequences but opposite orientations, only one of which is required for enhancer activity. Changes in both orientation and spacing of these sites substantially affect the activity of the CRM, as clusters of identical sites found in the Ciona genome with different arrangements are unable to activate transcription in notochord cells. This work presents the first evidence of a synergistic interaction between Brachyury and FoxA in the activation of an individual notochord CRM, and highlights the importance of transcription factor binding site arrangement for its function.
International Nuclear Information System (INIS)
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
2011-01-01
Highlights: → The sequences of -604 to -84 bp of the pUPII promoter contained the region of a putative negative cis-regulatory element. → The core promoter was located in the 5F-1. → Transcription factor HNF4 can directly bind in the pUPII core promoter region, which plays a critical role in controlling promoter activity. → These features of the pUPII promoter are fundamental to development of a target-specific vector. -- Abstract: 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.
Genetic mapping uncovers cis-regulatory landscape of RNA editing.
Ramaswami, Gokul; Deng, Patricia; Zhang, Rui; Anna Carbone, Mary; Mackay, Trudy F C; Li, Jin Billy
2015-09-16
Adenosine-to-inosine (A-to-I) RNA editing, catalysed by ADAR enzymes conserved in metazoans, plays an important role in neurological functions. Although the fine-tuning mechanism provided by A-to-I RNA editing is important, the underlying rules governing ADAR substrate recognition are not well understood. We apply a quantitative trait loci (QTL) mapping approach to identify genetic variants associated with variability in RNA editing. With very accurate measurement of RNA editing levels at 789 sites in 131 Drosophila melanogaster strains, here we identify 545 editing QTLs (edQTLs) associated with differences in RNA editing. We demonstrate that many edQTLs can act through changes in the local secondary structure for edited dsRNAs. Furthermore, we find that edQTLs located outside of the edited dsRNA duplex are enriched in secondary structure, suggesting that distal dsRNA structure beyond the editing site duplex affects RNA editing efficiency. Our work will facilitate the understanding of the cis-regulatory code of RNA editing.
Directory of Open Access Journals (Sweden)
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
Directory of Open Access Journals (Sweden)
Xu Fuyu
2012-09-01
Full Text Available Abstract Background The potential contribution of upstream sequence variation to the unique features of orthologous genes is just beginning to be unraveled. A core subset of stress-associated bZIP transcription factors from rice (Oryza sativa formed ten clusters of orthologous groups (COG with genes from the monocot sorghum (Sorghum bicolor and dicot Arabidopsis (Arabidopsis thaliana. The total cis-regulatory information content of each stress-associated COG was examined by phylogenetic footprinting to reveal ortholog-specific, lineage-specific and species-specific conservation patterns. Results The most apparent pattern observed was the occurrence of spatially conserved ‘core modules’ among the COGs but not among paralogs. These core modules are comprised of various combinations of two to four putative transcription factor binding site (TFBS classes associated with either developmental or stress-related functions. Outside the core modules are specific stress (ABA, oxidative, abiotic, biotic or organ-associated signals, which may be functioning as ‘regulatory fine-tuners’ and further define lineage-specific and species-specific cis-regulatory signatures. Orthologous monocot and dicot promoters have distinct TFBS classes involved in disease and oxidative-regulated expression, while the orthologous rice and sorghum promoters have distinct combinations of root-specific signals, a pattern that is not particularly conserved in Arabidopsis. Conclusions Patterns of cis-regulatory conservation imply that each ortholog has distinct signatures, further suggesting that they are potentially unique in a regulatory context despite the presumed conservation of broad biological function during speciation. Based on the observed patterns of conservation, we postulate that core modules are likely primary determinants of basal developmental programming, which may be integrated with and further elaborated by additional intrinsic or extrinsic signals in
Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.
Directory of Open Access Journals (Sweden)
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.
BET Bromodomain Inhibition Releases the Mediator Complex from Select cis-Regulatory Elements.
Bhagwat, Anand S; Roe, Jae-Seok; Mok, Beverly Y L; Hohmann, Anja F; Shi, Junwei; Vakoc, Christopher R
2016-04-19
The bromodomain and extraterminal (BET) protein BRD4 can physically interact with the Mediator complex, but the relevance of this association to the therapeutic effects of BET inhibitors in cancer is unclear. Here, we show that BET inhibition causes a rapid release of Mediator from a subset of cis-regulatory elements in the genome of acute myeloid leukemia (AML) cells. These sites of Mediator eviction were highly correlated with transcriptional suppression of neighboring genes, which are enriched for targets of the transcription factor MYB and for functions related to leukemogenesis. A shRNA screen of Mediator in AML cells identified the MED12, MED13, MED23, and MED24 subunits as performing a similar regulatory function to BRD4 in this context, including a shared role in sustaining a block in myeloid maturation. These findings suggest that the interaction between BRD4 and Mediator has functional importance for gene-specific transcriptional activation and for AML maintenance. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
Sun, Gao-Fei; He, Shou-Pu; Du, Xiong-Ming
2013-10-01
Cotton genomic studies have boomed since the release of Gossypium raimondii draft genome. In this study, cis-regulatory element (CRE) in 1 kb length sequence upstream 5' UTR of annotated genes were selected and scanned in the Arabidopsis thaliana (At) and Gossypium raimondii (Gr) genomes, based on the database of PLACE (Plant cis-acting Regulatory DNA Elements). According to the definition of this study, 44 (12.3%) and 57 (15.5%) CREs presented "peak-like" distribution in the 1 kb selected sequences of both genomes, respectively. Thirty-four of them were peak-like distributed in both genomes, which could be further categorized into 4 types based on their core sequences. The coincidence of TATABOX peak position and their actual position ((-) -30 bp) indicated that the position of a common CRE was conservative in different genes, which suggested that the peak position of these CREs was their possible actual position of transcription factors. The position of a common CRE was also different between the two genomes due to stronger length variation of 5' UTR in Gr than At. Furthermore, most of the peak-like CREs were located in the region of -110 bp-0 bp, which suggested that concentrated distribution might be conductive to the interaction of transcription factors, and then regulate the gene expression in downstream.
Combinatorial Cis-regulation in Saccharomyces Species
Directory of Open Access Journals (Sweden)
Aaron T. Spivak
2016-03-01
Full Text Available Transcriptional control of gene expression requires interactions between the cis-regulatory elements (CREs controlling gene promoters. We developed a sensitive computational method to identify CRE combinations with conserved spacing that does not require genome alignments. When applied to seven sensu stricto and sensu lato Saccharomyces species, 80% of the predicted interactions displayed some evidence of combinatorial transcriptional behavior in several existing datasets including: (1 chromatin immunoprecipitation data for colocalization of transcription factors, (2 gene expression data for coexpression of predicted regulatory targets, and (3 gene ontology databases for common pathway membership of predicted regulatory targets. We tested several predicted CRE interactions with chromatin immunoprecipitation experiments in a wild-type strain and strains in which a predicted cofactor was deleted. Our experiments confirmed that transcription factor (TF occupancy at the promoters of the CRE combination target genes depends on the predicted cofactor while occupancy of other promoters is independent of the predicted cofactor. Our method has the additional advantage of identifying regulatory differences between species. By analyzing the S. cerevisiae and S. bayanus genomes, we identified differences in combinatorial cis-regulation between the species and showed that the predicted changes in gene regulation explain several of the species-specific differences seen in gene expression datasets. In some instances, the same CRE combinations appear to regulate genes involved in distinct biological processes in the two different species. The results of this research demonstrate that (1 combinatorial cis-regulation can be inferred by multi-genome analysis and (2 combinatorial cis-regulation can explain differences in gene expression between species.
Multiple Functional Variants in cis Modulate PDYN Expression.
Babbitt, Courtney C; Silverman, Jesse S; Haygood, Ralph; Reininga, Jennifer M; Rockman, Matthew V; Wray, Gregory A
2010-02-01
Understanding genetic variation and its functional consequences within cis-regulatory regions remains an important challenge in human genetics and evolution. Here, we present a fine-scale functional analysis of segregating variation within the cis-regulatory region of prodynorphin, a gene that encodes an endogenous opioid precursor with roles in cognition and disease. In order to characterize the functional consequences of segregating variation in cis in a region under balancing selection in different human populations, we examined associations between specific polymorphisms and gene expression in vivo and in vitro. We identified five polymorphisms within the 5' flanking region that affect transcript abundance: a 68-bp repeat recognized in prior studies, as well as two microsatellites and two single nucleotide polymorphisms not previously implicated as functional variants. The impact of these variants on transcription differs by brain region, sex, and cell type, implying interactions between cis genotype and the differentiated state of cells. The effects of individual variants on expression level are not additive in some combinations, implying epistatic interactions between nearby variants. These data reveal an unexpectedly complex relationship between segregating genetic variation and its expression-trait consequences and highlights the importance of close functional scrutiny of natural genetic variation within even relatively well-studied cis-regulatory regions.
Changes in Cis-regulatory Elements during Morphological Evolution
Directory of Open Access Journals (Sweden)
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.
Characterization of Cer-1 cis-regulatory region during early Xenopus development.
Silva, Ana Cristina; Filipe, Mário; Steinbeisser, Herbert; Belo, José António
2011-05-01
Cerberus-related molecules are well-known Wnt, Nodal, and BMP inhibitors that have been implicated in different processes including anterior–posterior patterning and left–right asymmetry. In both mouse and frog, two Cerberus-related genes have been isolated, mCer-1 and mCer-2, and Xcer and Xcoco, respectively. Until now, little is known about the mechanisms involved in their transcriptional regulation. Here, we report a heterologous analysis of the mouse Cerberus-1 gene upstream regulatory regions, responsible for its expression in the visceral endodermal cells. Our analysis showed that the consensus sequences for a TATA, CAAT, or GC boxes were absent but a TGTGG sequence was present at position -172 to -168 bp, relative to the ATG. Using a series of deletion constructs and transient expression in Xenopus embryos, we found that a fragment of 1.4 kb of Cer-1 promoter sequence could reproduce the endogenous expression pattern of Xenopus cerberus. A 0.7-kb mcer-1 upstream region was able to drive reporter expression to the involuting mesendodermal cells, while further deletions abolished reporter gene expression. Our results suggest that although no sequence similarity was found between mouse and Xenopus cerberus cis-regulatory regions, the signaling cascades regulating cerberus expression, during gastrulation, is conserved.
A HLA class I cis-regulatory element whose activity can be modulated by hormones.
Sim, B C; Hui, K M
1994-12-01
To elucidate the basis of the down-regulation in major histocompatibility complex (MHC) class I gene expression and to identify possible DNA-binding regulatory elements that have the potential to interact with class I MHC genes, we have studied the transcriptional regulation of class I HLA genes in human breast carcinoma cells. A 9 base pair (bp) negative cis-regulatory element (NRE) has been identified using band-shift assays employing DNA sequences derived from the 5'-flanking region of HLA class I genes. This 9-bp element, GTCATGGCG, located within exon I of the HLA class I gene, can potently inhibit the expression of a heterologous thymidine kinase (TK) gene promoter and the HLA enhancer element. Furthermore, this regulatory element can exert its suppressive function in either the sense or anti-sense orientation. More interestingly, NRE can suppress dexamethasone-mediated gene activation in the context of the reported glucocorticoid-responsive element (GRE) in MCF-7 cells but has no influence on the estrogen-mediated transcriptional activation of MCF-7 cells in the context of the reported estrogen-responsive element (ERE). Furthermore, the presence of such a regulatory element within the HLA class I gene whose activity can be modulated by hormones correlates well with our observation that the level of HLA class I gene expression can be down-regulated by hormones in human breast carcinoma cells. Such interactions between negative regulatory elements and specific hormone trans-activators are novel and suggest a versatile form of transcriptional control.
Directory of Open Access Journals (Sweden)
Daniel Savic
Full Text Available Genome-wide association studies (GWAS have repeatedly shown an association between non-coding variants in the TCF7L2 locus and risk for type 2 diabetes (T2D, implicating a role for cis-regulatory variation within this locus in disease etiology. Supporting this hypothesis, we previously localized complex regulatory activity to the TCF7L2 T2D-associated interval using an in vivo bacterial artificial chromosome (BAC enhancer-trapping reporter strategy. To follow-up on this broad initial survey of the TCF7L2 regulatory landscape, we performed a fine-mapping enhancer scan using in vivo mouse transgenic reporter assays. We functionally interrogated approximately 50% of the sequences within the T2D-associated interval, utilizing sequence conservation within this 92-kb interval to determine the regulatory potential of all evolutionary conserved sequences that exhibited conservation to the non-eutherian mammal opossum. Included in this study was a detailed functional interrogation of sequences spanning both protective and risk alleles of single nucleotide polymorphism (SNP rs7903146, which has exhibited allele-specific enhancer function in pancreatic beta cells. Using these assays, we identified nine segments regulating various aspects of the TCF7L2 expression profile and that constitute nearly 70% of the sequences tested. These results highlight the regulatory complexity of this interval and support the notion that a TCF7L2 cis-regulatory disruption leads to T2D predisposition.
Lescot, Magali; Déhais, Patrice; Thijs, Gert; Marchal, Kathleen; Moreau, Yves; Van de Peer, Yves; Rouzé, Pierre; Rombauts, Stephane
2002-01-01
PlantCARE is a database of plant cis-acting regulatory elements, enhancers and repressors. Regulatory elements are represented by positional matrices, consensus sequences and individual sites on particular promoter sequences. Links to the EMBL, TRANSFAC and MEDLINE databases are provided when available. Data about the transcription sites are extracted mainly from the literature, supplemented with an increasing number of in silico predicted data. Apart from a general description for specific t...
PAA, WSH, and CIS Overview Self-Study #47656
Energy Technology Data Exchange (ETDEWEB)
Schroeder, Rachel Anne [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2017-09-14
This course presents an overview of the Department of Energy’s (DOE’s) regulatory requirements relevant to the Price-Anderson Amendments Act (PAAA, also referred to as nuclear safety), worker safety and health (WSH), and classified information security (CIS) that are enforceable under the DOE enforcement program; describes the DOE enforcement process; and provides an overview of Los Alamos National Laboratory’s (LANL’s) internal compliance program relative to these DOE regulatory requirements. The LANL PAAA Program is responsible for maintaining LANL’s internal compliance program, which ensures the prompt identification, screening, and reporting of noncompliances to DOE regulatory requirements pertaining to nuclear safety, WSH, and CIS to build the strongest mitigation position for the Laboratory with respect to civil or other penalties.
Directory of Open Access Journals (Sweden)
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.
Lmx1b-targeted cis-regulatory modules involved in limb dorsalization.
Haro, Endika; Watson, Billy A; Feenstra, Jennifer M; Tegeler, Luke; Pira, Charmaine U; Mohan, Subburaman; Oberg, Kerby C
2017-06-01
Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct gene targets in the limb have been confirmed. To determine direct targets, we performed a chromatin immunoprecipitation against Lmx1b in mouse limbs at embryonic day 12.5 followed by next-generation sequencing (ChIP-seq). Nearly 84% ( n =617) of the Lmx1b-bound genomic intervals (LBIs) identified overlap with chromatin regulatory marks indicative of potential cis -regulatory modules (PCRMs). In addition, 73 LBIs mapped to CRMs that are known to be active during limb development. We compared Lmx1b-bound PCRMs with genes regulated by Lmx1b and found 292 PCRMs within 1 Mb of 254 Lmx1b-regulated genes. Gene ontological analysis suggests that Lmx1b targets extracellular matrix production, bone/joint formation, axonal guidance, vascular development, cell proliferation and cell movement. We validated the functional activity of a PCRM associated with joint-related Gdf5 that provides a mechanism for Lmx1b-mediated joint modification and a PCRM associated with Lmx1b that suggests a role in autoregulation. This is the first report to describe genome-wide Lmx1b binding during limb development, directly linking Lmx1b to targets that accomplish limb dorsalization. © 2017. Published by The Company of Biologists Ltd.
Directory of Open Access Journals (Sweden)
Matloob Khushi
2014-11-01
Full Text Available Chromatin factors interact with each other in a cell and sequence-specific manner in order to regulate transcription and a wealth of publically available datasets exists describing the genomic locations of these interactions. Our recently published BiSA (Binding Sites Analyser database contains transcription factor binding locations and epigenetic modifications collected from published studies and provides tools to analyse stored and imported data. Using BiSA we investigated the overlapping cis-regulatory role of estrogen receptor alpha (ERα and progesterone receptor (PR in the T-47D breast cancer cell line. We found that ERα binding sites overlap with a subset of PR binding sites. To investigate further, we re-analysed raw data to remove any biases introduced by the use of distinct tools in the original publications. We identified 22,152 PR and 18,560 ERα binding sites (<5% false discovery rate with 4,358 overlapping regions among the two datasets. BiSA statistical analysis revealed a non-significant overall overlap correlation between the two factors, suggesting that ERα and PR are not partner factors and do not require each other for binding to occur. However, Monte Carlo simulation by Binary Interval Search (BITS, Relevant Distance, Absolute Distance, Jaccard and Projection tests by Genometricorr revealed a statistically significant spatial correlation of binding regions on chromosome between the two factors. Motif analysis revealed that the shared binding regions were enriched with binding motifs for ERα, PR and a number of other transcription and pioneer factors. Some of these factors are known to co-locate with ERα and PR binding. Therefore spatially close proximity of ERα binding sites with PR binding sites suggests that ERα and PR, in general function independently at the molecular level, but that their activities converge on a specific subset of transcriptional targets.
Thermodynamic state ensemble models of cis-regulation.
Directory of Open Access Journals (Sweden)
Marc S Sherman
Full Text Available A major goal in computational biology is to develop models that accurately predict a gene's expression from its surrounding regulatory DNA. Here we present one class of such models, thermodynamic state ensemble models. We describe the biochemical derivation of the thermodynamic framework in simple terms, and lay out the mathematical components that comprise each model. These components include (1 the possible states of a promoter, where a state is defined as a particular arrangement of transcription factors bound to a DNA promoter, (2 the binding constants that describe the affinity of the protein-protein and protein-DNA interactions that occur in each state, and (3 whether each state is capable of transcribing. Using these components, we demonstrate how to compute a cis-regulatory function that encodes the probability of a promoter being active. Our intention is to provide enough detail so that readers with little background in thermodynamics can compose their own cis-regulatory functions. To facilitate this goal, we also describe a matrix form of the model that can be easily coded in any programming language. This formalism has great flexibility, which we show by illustrating how phenomena such as competition between transcription factors and cooperativity are readily incorporated into these models. Using this framework, we also demonstrate that Michaelis-like functions, another class of cis-regulatory models, are a subset of the thermodynamic framework with specific assumptions. By recasting Michaelis-like functions as thermodynamic functions, we emphasize the relationship between these models and delineate the specific circumstances representable by each approach. Application of thermodynamic state ensemble models is likely to be an important tool in unraveling the physical basis of combinatorial cis-regulation and in generating formalisms that accurately predict gene expression from DNA sequence.
Transformation of Migration Flows Between the Russian Far East and CIS and non-CIS States
Directory of Open Access Journals (Sweden)
Motrich E. L.
2010-06-01
Full Text Available Basic trends in the migration processes in the Russian Far East are shown. Special emphasis is placed on the transformation of migration interactions with CIS and non-CIS countries both at the level of the region as a whole, and at the level of the Far Eastern territories of the Russian Federation. An extent of using foreign labor in different periods of the Russian Far East socio-economic development and the regulatory support of this process are shown. Prospects for attracting and utilizing foreign labor are stated
Suzuki, Masaharu; Ketterling, Matthew G; McCarty, Donald R
2005-09-01
We have developed a simple quantitative computational approach for objective analysis of cis-regulatory sequences in promoters of coregulated genes. The program, designated MotifFinder, identifies oligo sequences that are overrepresented in promoters of coregulated genes. We used this approach to analyze promoter sequences of Viviparous1 (VP1)/abscisic acid (ABA)-regulated genes and cold-regulated genes, respectively, of Arabidopsis (Arabidopsis thaliana). We detected significantly enriched sequences in up-regulated genes but not in down-regulated genes. This result suggests that gene activation but not repression is mediated by specific and common sequence elements in promoters. The enriched motifs include several known cis-regulatory sequences as well as previously unidentified motifs. With respect to known cis-elements, we dissected the flanking nucleotides of the core sequences of Sph element, ABA response elements (ABREs), and the C repeat/dehydration-responsive element. This analysis identified the motif variants that may correlate with qualitative and quantitative differences in gene expression. While both VP1 and cold responses are mediated in part by ABA signaling via ABREs, these responses correlate with unique ABRE variants distinguished by nucleotides flanking the ACGT core. ABRE and Sph motifs are tightly associated uniquely in the coregulated set of genes showing a strict dependence on VP1 and ABA signaling. Finally, analysis of distribution of the enriched sequences revealed a striking concentration of enriched motifs in a proximal 200-base region of VP1/ABA and cold-regulated promoters. Overall, each class of coregulated genes possesses a discrete set of the enriched motifs with unique distributions in their promoters that may account for the specificity of gene regulation.
Directory of Open Access Journals (Sweden)
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
Rigali, Sébastien; Anderssen, Sinaeda; Naômé, Aymeric; van Wezel, Gilles P
2018-01-05
The World Health Organization (WHO) describes antibiotic resistance as "one of the biggest threats to global health, food security, and development today", as the number of multi- and pan-resistant bacteria is rising dangerously. Acquired resistance phenomena also impair antifungals, antivirals, anti-cancer drug therapy, while herbicide resistance in weeds threatens the crop industry. On the positive side, it is likely that the chemical space of natural products goes far beyond what has currently been discovered. This idea is fueled by genome sequencing of microorganisms which unveiled numerous so-called cryptic biosynthetic gene clusters (BGCs), many of which are transcriptionally silent under laboratory culture conditions, and by the fact that most bacteria cannot yet be cultivated in the laboratory. However, brute force antibiotic discovery does not yield the same results as it did in the past, and researchers have had to develop creative strategies in order to unravel the hidden potential of microorganisms such as Streptomyces and other antibiotic-producing microorganisms. Identifying the cis elements and their corresponding transcription factors(s) involved in the control of BGCs through bioinformatic approaches is a promising strategy. Theoretically, we are a few 'clicks' away from unveiling the culturing conditions or genetic changes needed to activate the production of cryptic metabolites or increase the production yield of known compounds to make them economically viable. In this opinion article, we describe and illustrate the idea beyond 'cracking' the regulatory code for natural product discovery, by presenting a series of proofs of concept, and discuss what still should be achieved to increase the rate of success of this strategy. Copyright © 2018 Elsevier Inc. All rights reserved.
DEFF Research Database (Denmark)
Richards, Stephen; Liu, Yue; Bettencourt, Brian R.
2005-01-01
years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences......We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each...... between the species-but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence...
Fujibuchi, Wataru; Anderson, John S. J.; Landsman, David
2001-01-01
Consensus pattern and matrix-based searches designed to predict cis-acting transcriptional regulatory sequences have historically been subject to large numbers of false positives. We sought to decrease false positives by incorporating expression profile data into a consensus pattern-based search method. We have systematically analyzed the expression phenotypes of over 6000 yeast genes, across 121 expression profile experiments, and correlated them with the distribution of 14 known regulatory elements over sequences upstream of the genes. Our method is based on a metric we term probabilistic element assessment (PEA), which is a ranking of potential sites based on sequence similarity in the upstream regions of genes with similar expression phenotypes. For eight of the 14 known elements that we examined, our method had a much higher selectivity than a naïve consensus pattern search. Based on our analysis, we have developed a web-based tool called PROSPECT, which allows consensus pattern-based searching of gene clusters obtained from microarray data. PMID:11574681
Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila.
Directory of Open Access Journals (Sweden)
Margaret C W Ho
2009-11-01
Full Text Available It is a long-held belief in evolutionary biology that the rate of molecular evolution for a given DNA sequence is inversely related to the level of functional constraint. This belief holds true for the protein-coding homeotic (Hox genes originally discovered in Drosophila melanogaster. Expression of the Hox genes in Drosophila embryos is essential for body patterning and is controlled by an extensive array of cis-regulatory modules (CRMs. How the regulatory modules functionally evolve in different species is not clear. A comparison of the CRMs for the Abdominal-B gene from different Drosophila species reveals relatively low levels of overall sequence conservation. However, embryonic enhancer CRMs from other Drosophila species direct transgenic reporter gene expression in the same spatial and temporal patterns during development as their D. melanogaster orthologs. Bioinformatic analysis reveals the presence of short conserved sequences within defined CRMs, representing gap and pair-rule transcription factor binding sites. One predicted binding site for the gap transcription factor KRUPPEL in the IAB5 CRM was found to be altered in Superabdominal (Sab mutations. In Sab mutant flies, the third abdominal segment is transformed into a copy of the fifth abdominal segment. A model for KRUPPEL-mediated repression at this binding site is presented. These findings challenge our current understanding of the relationship between sequence evolution at the molecular level and functional activity of a CRM. While the overall sequence conservation at Drosophila CRMs is not distinctive from neighboring genomic regions, functionally critical transcription factor binding sites within embryonic enhancer CRMs are highly conserved. These results have implications for understanding mechanisms of gene expression during embryonic development, enhancer function, and the molecular evolution of eukaryotic regulatory modules.
Directory of Open Access Journals (Sweden)
Papaloukas Costas
2009-04-01
Full Text Available Abstract Background Polypeptides are composed of amino acids covalently bonded via a peptide bond. The majority of peptide bonds in proteins is found to occur in the trans conformation. In spite of their infrequent occurrence, cis peptide bonds play a key role in the protein structure and function, as well as in many significant biological processes. Results We perform a systematic analysis of regions in protein sequences that contain a proline cis peptide bond in order to discover non-random associations between the primary sequence and the nature of proline cis/trans isomerization. For this purpose an efficient pattern discovery algorithm is employed which discovers regular expression-type patterns that are overrepresented (i.e. appear frequently repeated in a set of sequences. Four types of pattern discovery are performed: i exact pattern discovery, ii pattern discovery using a chemical equivalency set, iii pattern discovery using a structural equivalency set and iv pattern discovery using certain amino acids' physicochemical properties. The extracted patterns are carefully validated using a specially implemented scoring function and a significance measure (i.e. log-probability estimate indicative of their specificity. The score threshold for the first three types of pattern discovery is 0.90 while for the last type of pattern discovery 0.80. Regarding the significance measure, all patterns yielded values in the range [-9, -31] which ensure that the derived patterns are highly unlikely to have emerged by chance. Among the highest scoring patterns, most of them are consistent with previous investigations concerning the neighborhood of cis proline peptide bonds, and many new ones are identified. Finally, the extracted patterns are systematically compared against the PROSITE database, in order to gain insight into the functional implications of cis prolyl bonds. Conclusion Cis patterns with matches in the PROSITE database fell mostly into two
Weterings, K; Schrauwen, J; Wullems, G; Twell, D
1995-07-01
Regulatory elements within the promoter of the pollen-specific NTP303 gene from tobacco were analysed by transient and stable expression analyses. Analysis of precisely targeted mutations showed that the NTP303 promoter is not regulated by any of the previously described pollen-specific cis-regulatory elements. However, two adjacent regions from -103 to -86 bp and from -86 to -59 bp were shown to contain sequences which positively regulated the NTP303 promoter. Both of these regions were capable of driving pollen-specific expression from a heterologous promoter, independent of orientation and in an additive manner. The boundaries of the minimal, functional NTP303 promoter were determined to lie within the region -86 to -51 bp. The sequence AAATGA localized from -94 to -89 bp was identified as a novel cis-acting element, of which the TGA triplet was shown to comprise an active part. This element was shown to be completely conserved in the similarly regulated promoter of the Bp 10 gene from Brassica napus encoding a homologue of the NTP303 gene.
Directory of Open Access Journals (Sweden)
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
Directory of Open Access Journals (Sweden)
Mohammed Bakkali
Full Text Available The importance of non-coding DNAs that control transcription is ever noticeable, but the characterization and analysis of the evolution of such DNAs presents challenges not found in the analysis of coding sequences. In this study of the cis-regulatory elements of the pair rule segmentation gene fushi tarazu (ftz I report the DNA sequences of ftz's zebra element (promoter and a region containing the proximal enhancer from a total of 45 fly lines belonging to several populations of the species Drosophila melanogaster, D. simulans, D. sechellia, D. mauritiana, D. yakuba, D. teissieri, D. orena and D. erecta. Both elements evolve at slower rate than ftz synonymous sites, thus reflecting their functional importance. The promoter evolves more slowly than the average for ftz's coding sequence while, on average, the enhancer evolves more rapidly, suggesting more functional constraint and effective purifying selection on the former. Comparative analysis of the number and nature of base substitutions failed to detect significant evidence for positive/adaptive selection in transcription-factor-binding sites. These seem to evolve at similar rates to regions not known to bind transcription factors. Although this result reflects the evolutionary flexibility of the transcription factor binding sites, it also suggests a complex and still not completely understood nature of even the characterized cis-regulatory sequences. The latter seem to contain more functional parts than those currently identified, some of which probably transcription factor binding. This study illustrates ways in which functional assignments of sequences within cis-acting sequences can be used in the search for adaptive evolution, but also highlights difficulties in how such functional assignment and analysis can be carried out.
Dean, Kimberly M; Grayhack, Elizabeth J
2012-12-01
We have developed a robust and sensitive method, called RNA-ID, to screen for cis-regulatory sequences in RNA using fluorescence-activated cell sorting (FACS) of yeast cells bearing a reporter in which expression of both superfolder green fluorescent protein (GFP) and yeast codon-optimized mCherry red fluorescent protein (RFP) is driven by the bidirectional GAL1,10 promoter. This method recapitulates previously reported progressive inhibition of translation mediated by increasing numbers of CGA codon pairs, and restoration of expression by introduction of a tRNA with an anticodon that base pairs exactly with the CGA codon. This method also reproduces effects of paromomycin and context on stop codon read-through. Five key features of this method contribute to its effectiveness as a selection for regulatory sequences: The system exhibits greater than a 250-fold dynamic range, a quantitative and dose-dependent response to known inhibitory sequences, exquisite resolution that allows nearly complete physical separation of distinct populations, and a reproducible signal between different cells transformed with the identical reporter, all of which are coupled with simple methods involving ligation-independent cloning, to create large libraries. Moreover, we provide evidence that there are sequences within a 9-nt library that cause reduced GFP fluorescence, suggesting that there are novel cis-regulatory sequences to be found even in this short sequence space. This method is widely applicable to the study of both RNA-mediated and codon-mediated effects on expression.
Neuman, Sarah D.; Bashirullah, Arash; Kumar, Justin P.
2016-01-01
The eyes absent (eya) gene of the fruit fly, Drosophila melanogaster, is a member of an evolutionarily conserved gene regulatory network that controls eye formation in all seeing animals. The loss of eya leads to the complete elimination of the compound eye while forced expression of eya in non-retinal tissues is sufficient to induce ectopic eye formation. Within the developing retina eya is expressed in a dynamic pattern and is involved in tissue specification/determination, cell proliferation, apoptosis, and cell fate choice. In this report we explore the mechanisms by which eya expression is spatially and temporally governed in the developing eye. We demonstrate that multiple cis-regulatory elements function cooperatively to control eya transcription and that spacing between a pair of enhancer elements is important for maintaining correct gene expression. Lastly, we show that the loss of eya expression in sine oculis (so) mutants is the result of massive cell death and a progressive homeotic transformation of retinal progenitor cells into head epidermis. PMID:27930646
Yin, Tao; Wu, Hanying; Zhang, Shanglong; Lu, Hongyu; Zhang, Lingxiao; Xu, Yong; Chen, Daming; Liu, Jingmei
2009-01-01
A 1.8 kb 5'-flanking region of the large subunit of ADP-glucose pyrophosphorylase, isolated from watermelon (Citrullus vulgaris S.), has fruit-specific promoter activity in transgenic tomato plants. Two negative regulatory regions, from -986 to -959 and from -472 to -424, were identified in this promoter region by fine deletion analyses. Removal of both regions led to constitutive expression in epidermal cells. Gain-of-function experiments showed that these two regions were sufficient to inhibit RFP (red fluorescent protein) expression in transformed epidermal cells when fused to the cauliflower mosaic virus (CaMV) 35S minimal promoter. Gel mobility shift experiments demonstrated the presence of leaf nuclear factors that interact with these two elements. A TCCAAAA motif was identified in these two regions, as well as one in the reverse orientation, which was confirmed to be a novel specific cis-element. A quantitative beta-glucuronidase (GUS) activity assay of stable transgenic tomato plants showed that the activities of chimeric promoters harbouring only one of the two cis-elements, or both, were approximately 10-fold higher in fruits than in leaves. These data confirm that the TCCAAAA motif functions as a fruit-specific element by inhibiting gene expression in leaves.
Video encoder/decoder for encoding/decoding motion compensated images
1996-01-01
Video encoder and decoder, provided with a motion compensator for motion-compensated video coding or decoding in which a picture is coded or decoded in blocks in alternately horizontal and vertical steps. The motion compensator is provided with addressing means (160) and controlled multiplexers
Liseron-Monfils, Christophe; Lewis, Tim; Ashlock, Daniel; McNicholas, Paul D; Fauteux, François; Strömvik, Martina; Raizada, Manish N
2013-03-15
The discovery of genetic networks and cis-acting DNA motifs underlying their regulation is a major objective of transcriptome studies. The recent release of the maize genome (Zea mays L.) has facilitated in silico searches for regulatory motifs. Several algorithms exist to predict cis-acting elements, but none have been adapted for maize. A benchmark data set was used to evaluate the accuracy of three motif discovery programs: BioProspector, Weeder and MEME. Analysis showed that each motif discovery tool had limited accuracy and appeared to retrieve a distinct set of motifs. Therefore, using the benchmark, statistical filters were optimized to reduce the false discovery ratio, and then remaining motifs from all programs were combined to improve motif prediction. These principles were integrated into a user-friendly pipeline for motif discovery in maize called Promzea, available at http://www.promzea.org and on the Discovery Environment of the iPlant Collaborative website. Promzea was subsequently expanded to include rice and Arabidopsis. Within Promzea, a user enters cDNA sequences or gene IDs; corresponding upstream sequences are retrieved from the maize genome. Predicted motifs are filtered, combined and ranked. Promzea searches the chosen plant genome for genes containing each candidate motif, providing the user with the gene list and corresponding gene annotations. Promzea was validated in silico using a benchmark data set: the Promzea pipeline showed a 22% increase in nucleotide sensitivity compared to the best standalone program tool, Weeder, with equivalent nucleotide specificity. Promzea was also validated by its ability to retrieve the experimentally defined binding sites of transcription factors that regulate the maize anthocyanin and phlobaphene biosynthetic pathways. Promzea predicted additional promoter motifs, and genome-wide motif searches by Promzea identified 127 non-anthocyanin/phlobaphene genes that each contained all five predicted promoter
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
On minimizing the maximum broadcast decoding delay for instantly decodable network coding
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.
On minimizing the maximum broadcast decoding delay for instantly decodable network coding
Douik, Ahmed S.; Sorour, Sameh; Alouini, Mohamed-Slim; Ai-Naffouri, Tareq Y.
2014-01-01
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
MicroRNA signature of cis-platin resistant vs. cis-platin sensitive ovarian cancer cell lines
Directory of Open Access Journals (Sweden)
Kumar Smriti
2011-09-01
Full Text Available Abstract Background Ovarian cancer is the leading cause of death from gynecologic cancer in women worldwide. According to the National Cancer Institute, ovarian cancer has the highest mortality rate among all the reproductive cancers in women. Advanced stage diagnosis and chemo/radio-resistance is a major obstacle in treating advanced ovarian cancer. The most commonly employed chemotherapeutic drug for ovarian cancer treatment is cis-platin. As with most chemotherapeutic drugs, many patients eventually become resistant to cis-platin and therefore, diminishing its effect. The efficacy of current treatments may be improved by increasing the sensitivity of cancer cells to chemo/radiation therapies. Methods The present study is focused on identifying the differential expression of regulatory microRNAs (miRNAs between cis-platin sensitive (A2780, and cis-platin resistant (A2780/CP70 cell lines. Cell proliferation assays were conducted to test the sensitivity of the two cell lines to cis-platin. Differential expression patterns of miRNA between cis-platin sensitive and cis-platin resistant cell lines were analyzed using novel LNA technology. Results Our results revealed changes in expression of 11 miRNAs out of 1,500 miRNAs analyzed. Out of the 11 miRNAs identified, 5 were up-regulated in the A2780/CP70 cell line and 6 were down regulated as compared to cis-platin sensitive A2780 cells. Our microRNA data was further validated by quantitative real-time PCR for these selected miRNAs. Ingenuity Pathway Analysis (IPA and Kyoto Encyclopedia of Genes and Genomes (KEGG analysis was performed for the selected miRNAs and their putative targets to identify the potential pathways and networks involved in cis-platin resistance. Conclusions Our data clearly showed the differential expression of 11 miRNAs in cis-platin resistant cells, which could potentially target many important pathways including MAPK, TGF-β signaling, actin cytoskeleton, ubiquitin mediated
Cis-regulatory timers for developmental gene expression.
Directory of Open Access Journals (Sweden)
Lionel Christiaen
2013-10-01
Full Text Available How does a fertilized egg decode its own genome to eventually develop into a mature animal? Each developing cell must activate a battery of genes in a timely manner and according to the function it will ultimately perform, but how? During development of the notochord--a structure akin to the vertebrate spine--in a simple marine invertebrate, an essential protein called Brachyury binds to specific sites in its target genes. A study just published in PLOS Biology reports that if the target gene contains multiple Brachyury-binding sites it will be activated early in development but if it contains only one site it will be activated later. Genes that contain no binding site can still be activated by Brachyury, but only indirectly by an earlier Brachyury-dependent gene product, so later than the directly activated genes. Thus, this study shows how several genes can interpret the presence of a single factor differently to become active at distinct times in development.
Decoding of interleaved Reed-Solomon codes using improved power decoding
DEFF Research Database (Denmark)
Puchinger, Sven; Rosenkilde ne Nielsen, Johan
2017-01-01
We propose a new partial decoding algorithm for m-interleaved Reed-Solomon (IRS) codes that can decode, with high probability, a random error of relative weight 1 − Rm/m+1 at all code rates R, in time polynomial in the code length n. For m > 2, this is an asymptotic improvement over the previous...... state-of-the-art for all rates, and the first improvement for R > 1/3 in the last 20 years. The method combines collaborative decoding of IRS codes with power decoding up to the Johnson radius....
Low-Power Bitstream-Residual Decoder for H.264/AVC Baseline Profile Decoding
Directory of Open Access Journals (Sweden)
Xu Ke
2009-01-01
Full Text Available Abstract We present the design and VLSI implementation of a novel low-power bitstream-residual decoder for H.264/AVC baseline profile. It comprises a syntax parser, a parameter decoder, and an Inverse Quantization Inverse Transform (IQIT decoder. The syntax parser detects and decodes each incoming codeword in the bitstream under the control of a hierarchical Finite State Machine (FSM; the IQIT decoder performs inverse transform and quantization with pipelining and parallelism. Various power reduction techniques, such as data-driven based on statistic results, nonuniform partition, precomputation, guarded evaluation, hierarchical FSM decomposition, TAG method, zero-block skipping, and clock gating , are adopted and integrated throughout the bitstream-residual decoder. With innovative architecture, the proposed design is able to decode QCIF video sequences of 30 fps at a clock rate as low as 1.5 MHz. A prototype H.264/AVC baseline decoding chip utilizing the proposed decoder is fabricated in UMC 0.18 m 1P6M CMOS technology. The proposed design is measured under 1 V 1.8 V supply with 0.1 V step. It dissipates 76 W at 1 V and 253 W at 1.8 V.
Investment in the CEE/CIS region
International Nuclear Information System (INIS)
Lemierre, J.
2002-01-01
The energy investments in the Central and Eastern European region and the Commonwealth of Independent States (CIS) region are discussed in this Keynote Address. The message is addressed to regulators and governments. The restructuring of old industries to save energy is highlighted. The regulatory system must undergo a substantial reform. Another message is placed for investors in the energy field. (R.P.)
Energy Technology Data Exchange (ETDEWEB)
Zheng, Xueyun; Renslow, Ryan S.; Makola, Mpho M.; Webb, Ian K.; Deng, Liulin; Thomas, Dennis G.; Govind, Niranjan; Ibrahim, Yehia M.; Kabanda, Mwadham M.; Dubery, Ian A.; Heyman, Heino M.; Smith, Richard D.; Madala, Ntakadzeni E.; Baker, Erin S.
2017-03-15
Due to the recently uncovered health benefits and anti-HIV activities of dicaffeoylquinic acids (diCQAs), understanding their structures and functions is of great interest for drug discovery efforts. DiCQAs are analytically challenging to identify and quantify since they commonly exist as a diverse mixture of positional and geometric (cis/trans) isomers. In this work, we utilized ion mobility spectrometry coupled with mass spectrometry to separate the various isomers before and after UV irradiation. The experimental collision cross sections were then compared with theoretical structures to differentiate and identify the diCQA isomers. Our analyses found that naturally the diCQAs existed predominantly as trans/trans isomers, but after 3 h of UV irradiation, cis/cis, cis/trans, trans/cis, and trans/trans isomers were all present in the mixture. This is the first report of successful differentiation of cis/trans diCQA isomers individually, which shows the great promise of IMS coupled with theoretical calculations for determining the structure and activity relationships of different isomers in drug discovery studies.
Completion time reduction in instantly decodable network coding through decoding delay control
Douik, Ahmed S.; Sorour, Sameh; Alouini, Mohamed-Slim; Al-Naffouri, Tareq Y.
2014-01-01
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.
Completion time reduction in instantly decodable network coding through decoding delay control
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.
Directory of Open Access Journals (Sweden)
Gabriel Castrillo
Full Text Available Transcriptional regulation is an important mechanism underlying gene expression and has played a crucial role in evolution. The number, position and interactions between cis-elements and transcription factors (TFs determine the expression pattern of a gene. To identify functionally relevant cis-elements in gene promoters, a phylogenetic shadowing approach with a lipase gene (LIP1 was used. As a proof of concept, in silico analyses of several Brassicaceae LIP1 promoters identified a highly conserved sequence (LIP1 element that is sufficient to drive strong expression of a reporter gene in planta. A collection of ca. 1,200 Arabidopsis thaliana TF open reading frames (ORFs was arrayed in a 96-well format (RR library and a convenient mating based yeast one hybrid (Y1H screening procedure was established. We constructed an episomal plasmid (pTUY1H to clone the LIP1 element and used it as bait for Y1H screenings. A novel interaction with an HD-ZIP (AtML1 TF was identified and abolished by a 2 bp mutation in the LIP1 element. A role of this interaction in transcriptional regulation was confirmed in planta. In addition, we validated our strategy by reproducing the previously reported interaction between a MYB-CC (PHR1 TF, a central regulator of phosphate starvation responses, with a conserved promoter fragment (IPS1 element containing its cognate binding sequence. Finally, we established that the LIP1 and IPS1 elements were differentially bound by HD-ZIP and MYB-CC family members in agreement with their genetic redundancy in planta. In conclusion, combining in silico analyses of orthologous gene promoters with Y1H screening of the RR library represents a powerful approach to decipher cis- and trans-regulatory codes.
Academic Training - Bioinformatics: Decoding the Genome
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...
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....
Adaptive decoding of convolutional codes
Hueske, K.; Geldmacher, J.; Götze, J.
2007-06-01
Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.
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....
Adaptive decoding of convolutional codes
Directory of Open Access Journals (Sweden)
K. Hueske
2007-06-01
Full Text Available Convolutional codes, which are frequently used as error correction codes in digital transmission systems, are generally decoded using the Viterbi Decoder. On the one hand the Viterbi Decoder is an optimum maximum likelihood decoder, i.e. the most probable transmitted code sequence is obtained. On the other hand the mathematical complexity of the algorithm only depends on the used code, not on the number of transmission errors. To reduce the complexity of the decoding process for good transmission conditions, an alternative syndrome based decoder is presented. The reduction of complexity is realized by two different approaches, the syndrome zero sequence deactivation and the path metric equalization. The two approaches enable an easy adaptation of the decoding complexity for different transmission conditions, which results in a trade-off between decoding complexity and error correction performance.
Energy Technology Data Exchange (ETDEWEB)
Richards, Stephen; Liu, Yue; Bettencourt, Brian R.; Hradecky, Pavel; Letovsky, Stan; Nielsen, Rasmus; Thornton, Kevin; Todd, Melissa J.; Chen, Rui; Meisel, Richard P.; Couronne, Olivier; Hua, Sujun; Smith, Mark A.; Bussemaker, Harmen J.; van Batenburg, Marinus F.; Howells, Sally L.; Scherer, Steven E.; Sodergren, Erica; Matthews, Beverly B.; Crosby, Madeline A.; Schroeder, Andrew J.; Ortiz-Barrientos, Daniel; Rives, Catherine M.; Metzker, Michael L.; Muzny, Donna M.; Scott, Graham; Steffen, David; Wheeler, David A.; Worley, Kim C.; Havlak, Paul; Durbin, K. James; Egan, Amy; Gill, Rachel; Hume, Jennifer; Morgan, Margaret B.; Miner, George; Hamilton, Cerissa; Huang, Yanmei; Waldron, Lenee; Verduzco, Daniel; Blankenburg, Kerstin P.; Dubchak, Inna; Noor, Mohamed A.F.; Anderson, Wyatt; White, Kevin P.; Clark, Andrew G.; Schaeffer, Stephen W.; Gelbart, William; Weinstock, George M.; Gibbs, Richard A.
2004-04-01
The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have remained on the same arm, but within each arm gene order has been extensively reshuffled leading to the identification of approximately 1300 syntenic blocks. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 35 My since divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome wide average consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than control sequences between the species but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a picture of repeat mediated chromosomal rearrangement, and high co-adaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila.
Directory of Open Access Journals (Sweden)
Lamprini G Kalampoki
Full Text Available Coup-TF, an orphan member of the nuclear receptor super family, has a fundamental role in the development of metazoan embryos. The study of the gene's regulatory circuit in the sea urchin embryo will facilitate the placement of this transcription factor in the well-studied embryonic Gene Regulatory Network (GRN. The Paracentrotus lividus Coup-TF gene (PlCoup-TF is expressed throughout embryonic development preferentially in the oral ectoderm of the gastrula and the ciliary band of the pluteus stage. Two overlapping λ genomic clones, containing three exons and upstream sequences of PlCoup-TF, were isolated from a genomic library. The transcription initiation site was determined and 5' deletions and individual segments of a 1930 bp upstream region were placed ahead of a GFP reporter cassette and injected into fertilized P.lividus eggs. Module a (-532 to -232, was necessary and sufficient to confer ciliary band expression to the reporter. Comparison of P.lividus and Strongylocentrotus purpuratus upstream Coup-TF sequences, revealed considerable conservation, but none within module a. 5' and internal deletions into module a, defined a smaller region that confers ciliary band specific expression. Putative regulatory cis-acting elements (RE1, RE2 and RE3 within module a, were specifically bound by proteins in sea urchin embryonic nuclear extracts. Site-specific mutagenesis of these elements resulted in loss of reporter activity (RE1 or ectopic expression (RE2, RE3. It is proposed that sea urchin transcription factors, which bind these three regulatory sites, are necessary for spatial and quantitative regulation of the PlCoup-TF gene at pluteus stage sea urchin embryos. These findings lead to the future identification of these factors and to the hierarchical positioning of PlCoup-TF within the embryonic GRN.
DEFF Research Database (Denmark)
Farooq, Muhammad; Troelsen, Jesper T; Boyd, Mette
2010-01-01
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...... demonstrated a marked difference between wild-type and the mutant probe, which uniquely bound one or several transcription factors extracted from Caco-2 cells. This finding supports a model in which ectopic anterior SHH expression in the developing limb results from abnormal binding of one or more...
PReMod: a database of genome-wide mammalian cis-regulatory module predictions.
Ferretti, Vincent; Poitras, Christian; Bergeron, Dominique; Coulombe, Benoit; Robert, François; Blanchette, Mathieu
2007-01-01
We describe PReMod, a new database of genome-wide cis-regulatory module (CRM) predictions for both the human and the mouse genomes. The prediction algorithm, described previously in Blanchette et al. (2006) Genome Res., 16, 656-668, exploits the fact that many known CRMs are made of clusters of phylogenetically conserved and repeated transcription factors (TF) binding sites. Contrary to other existing databases, PReMod is not restricted to modules located proximal to genes, but in fact mostly contains distal predicted CRMs (pCRMs). Through its web interface, PReMod allows users to (i) identify pCRMs around a gene of interest; (ii) identify pCRMs that have binding sites for a given TF (or a set of TFs) or (iii) download the entire dataset for local analyses. Queries can also be refined by filtering for specific chromosomal regions, for specific regions relative to genes or for the presence of CpG islands. The output includes information about the binding sites predicted within the selected pCRMs, and a graphical display of their distribution within the pCRMs. It also provides a visual depiction of the chromosomal context of the selected pCRMs in terms of neighboring pCRMs and genes, all of which are linked to the UCSC Genome Browser and the NCBI. PReMod: http://genomequebec.mcgill.ca/PReMod.
Olenkina, O M; Egorova, K S; Aravin, A A; Naumova, N M; Gvozdev, V A; Olenina, L V
2012-11-01
Tandem Stellate genes organized into two clusters in heterochromatin and euchromatin of the X-chromosome are part of the Ste-Su(Ste) genetic system required for maintenance of male fertility and reproduction of Drosophila melanogaster. Stellate genes encode a regulatory subunit of protein kinase CK2 and are the main targets of germline-specific piRNA-silencing; their derepression leads to appearance of protein crystals in spermatocytes, meiotic disturbances, and male sterility. A short promoter region of 134 bp appears to be sufficient for testis-specific transcription of Stellate, and it contains three closely located cis-regulatory elements called E-boxes. By using reporter analysis, we confirmed a strong functionality of the E-boxes in the Stellate promoter for in vivo transcription. Using selective mutagenesis, we have shown that the presence of the central E-box 2 is preferable to maintain a high-level testis-specific transcription of the reporter gene under the Stellate promoter. The Stellate promoter provides transcription even in heterochromatin, and corresponding mRNAs are translated with the generation of full-size protein products in case of disturbances in the piRNA-silencing process. We have also shown for the first time that the activity of the Stellate promoter is determined by chromatin context of the X-chromosome in male germinal cells, and it increases at about twofold when relocating in autosomes.
Decoding Facial Expressions: A New Test with Decoding Norms.
Leathers, Dale G.; Emigh, Ted H.
1980-01-01
Describes the development and testing of a new facial meaning sensitivity test designed to determine how specialized are the meanings that can be decoded from facial expressions. Demonstrates the use of the test to measure a receiver's current level of skill in decoding facial expressions. (JMF)
Identifying Cis-Regulatory Changes Involved in the Evolution of Aerobic Fermentation in Yeasts
Lin, Zhenguo; Wang, Tzi-Yuan; Tsai, Bing-Shi; Wu, Fang-Ting; Yu, Fu-Jung; Tseng, Yu-Jung; Sung, Huang-Mo; Li, Wen-Hsiung
2013-01-01
Gene regulation change has long been recognized as an important mechanism for phenotypic evolution. We used the evolution of yeast aerobic fermentation as a model to explore how gene regulation has evolved and how this process has contributed to phenotypic evolution and adaptation. Most eukaryotes fully oxidize glucose to CO2 and H2O in mitochondria to maximize energy yield, whereas some yeasts, such as Saccharomyces cerevisiae and its relatives, predominantly ferment glucose into ethanol even in the presence of oxygen, a phenomenon known as aerobic fermentation. We examined the genome-wide gene expression levels among 12 different yeasts and found that a group of genes involved in the mitochondrial respiration process showed the largest reduction in gene expression level during the evolution of aerobic fermentation. Our analysis revealed that the downregulation of these genes was significantly associated with massive loss of binding motifs of Cbf1p in the fermentative yeasts. Our experimental assays confirmed the binding of Cbf1p to the predicted motif and the activator role of Cbf1p. In summary, our study laid a foundation to unravel the long-time mystery about the genetic basis of evolution of aerobic fermentation, providing new insights into understanding the role of cis-regulatory changes in phenotypic evolution. PMID:23650209
Forced Sequence Sequential Decoding
DEFF Research Database (Denmark)
Jensen, Ole Riis; Paaske, Erik
1998-01-01
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 (RS) codes with nonuniform profile. With this scheme decoding with good performance is possible as low...... as Eb/N0=0.6 dB, which is about 1.25 dB below the signal-to-noise ratio (SNR) that marks the cutoff rate for the full system. Accounting for about 0.45 dB due to the outer codes, sequential decoding takes place at about 1.7 dB below the SNR cutoff rate for the convolutional code. This is possible since...... 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...
Directory of Open Access Journals (Sweden)
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
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. © The Author(s) 2011. Published by Oxford University Press.
Rosinski-Chupin, Isabelle; Sauvage, Elisabeth; Sismeiro, Odile; Villain, Adrien; Da Cunha, Violette; Caliot, Marie-Elise; Dillies, Marie-Agnès; Trieu-Cuot, Patrick; Bouloc, Philippe; Lartigue, Marie-Frédérique; Glaser, Philippe
2015-05-30
Streptococcus agalactiae, or Group B Streptococcus, is a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. In an effort to reconstruct the transcriptional networks involved in S. agalactiae physiology and pathogenesis, we performed an extensive and robust characterization of its transcriptome through a combination of differential RNA-sequencing in eight different growth conditions or genetic backgrounds and strand-specific RNA-sequencing. Our study identified 1,210 transcription start sites (TSSs) and 655 transcript ends as well as 39 riboswitches and cis-regulatory regions, 39 cis-antisense non-coding RNAs and 47 small RNAs potentially acting in trans. Among these putative regulatory RNAs, ten were differentially expressed in response to an acid stress and two riboswitches sensed directly or indirectly the pH modification. Strikingly, 15% of the TSSs identified were associated with the incorporation of pseudo-templated nucleotides, showing that reiterative transcription is a pervasive process in S. agalactiae. In particular, 40% of the TSSs upstream genes involved in nucleotide metabolism show reiterative transcription potentially regulating gene expression, as exemplified for pyrG and thyA encoding the CTP synthase and the thymidylate synthase respectively. This comprehensive map of the transcriptome at the single nucleotide resolution led to the discovery of new regulatory mechanisms in S. agalactiae. It also provides the basis for in depth analyses of transcriptional networks in S. agalactiae and of the regulatory role of reiterative transcription following variations of intra-cellular nucleotide pools.
International Nuclear Information System (INIS)
Wang, Xuting; Tomso, Daniel J.; Liu Xuemei; Bell, Douglas A.
2005-01-01
Single nucleotide polymorphisms (SNPs) in the human genome are DNA sequence variations that can alter an individual's response to environmental exposure. SNPs in gene coding regions can lead to changes in the biological properties of the encoded protein. In contrast, SNPs in non-coding gene regulatory regions may affect gene expression levels in an allele-specific manner, and these functional polymorphisms represent an important but relatively unexplored class of genetic variation. The main challenge in analyzing these SNPs is a lack of robust computational and experimental methods. Here, we first outline mechanisms by which genetic variation can impact gene regulation, and review recent findings in this area; then, we describe a methodology for bioinformatic discovery and functional analysis of regulatory SNPs in cis-regulatory regions using the assembled human genome sequence and databases on sequence polymorphism and gene expression. Our method integrates SNP and gene databases and uses a set of computer programs that allow us to: (1) select SNPs, from among the >9 million human SNPs in the NCBI dbSNP database, that are similar to cis-regulatory element (RE) consensus sequences; (2) map the selected dbSNP entries to the human genome assembly in order to identify polymorphic REs near gene start sites; (3) prioritize the candidate polymorphic RE containing genes by searching the existing genotype and gene expression data sets. The applicability of this system has been demonstrated through studies on p53 responsive elements and is being extended to additional pathways and environmentally responsive genes
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 possible as low as Eb/No=0.6 dB, which is about 1.7 dB below the signal-to-noise ratio that marks the cut-off rate for the convolutional code. This is possible since 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 Reed-Solomon word is decoded after C computations are presented. This is supported by simulation results that are also extended to other parameters....
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....
Directory of Open Access Journals (Sweden)
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
Wilding, Craig S; Smith, Ian; Lynd, Amy; Yawson, Alexander Egyir; Weetman, David; Paine, Mark J I; Donnelly, Martin J
2012-09-01
Although cytochrome P450 (CYP450) enzymes are frequently up-regulated in mosquitoes resistant to insecticides, no regulatory motifs driving these expression differences with relevance to wild populations have been identified. Transposable elements (TEs) are often enriched upstream of those CYP450s involved in insecticide resistance, leading to the assumption that they contribute regulatory motifs that directly underlie the resistance phenotype. A partial CuRE1 (Culex Repetitive Element 1) transposable element is found directly upstream of CYP9M10, a cytochrome P450 implicated previously in larval resistance to permethrin in the ISOP450 strain of Culex quinquefasciatus, but is absent from the equivalent genomic region of a susceptible strain. Via expression of CYP9M10 in Escherichia coli we have now demonstrated time- and NADPH-dependant permethrin metabolism, prerequisites for confirmation of a role in metabolic resistance, and through qPCR shown that CYP9M10 is >20-fold over-expressed in ISOP450 compared to a susceptible strain. In a fluorescent reporter assay the region upstream of CYP9M10 from ISOP450 drove 10× expression compared to the equivalent region (lacking CuRE1) from the susceptible strain. Close correspondence with the gene expression fold-change implicates the upstream region including CuRE1 as a cis-regulatory element involved in resistance. Only a single CuRE1 bearing allele, identical to the CuRE1 bearing allele in the resistant strain, is found throughout Sub-Saharan Africa, in contrast to the diversity encountered in non-CuRE1 alleles. This suggests a single origin and subsequent spread due to selective advantage. CuRE1 is detectable using a simple diagnostic. When applied to C. quinquefasciatus larvae from Ghana we have demonstrated a significant association with permethrin resistance in multiple field sites (mean Odds Ratio = 3.86) suggesting this marker has relevance to natural populations of vector mosquitoes. However, when CuRE1 was excised
Bekiaris, Pavlos Stephanos; Tekath, Tobias; Staiger, Dorothee; Danisman, Selahattin
2018-01-01
Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, "Exploration of Distinctive CREs and CRMs" (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, "CRM Network Generator" (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression.
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...... Hermitian codes using Guruswami–Sudan or Power decoding faster than previously known, and we show how to Wu list decode binary Goppa codes....... to solve such using module minimisation, or using our new Demand–Driven algorithm which is also based on module minimisation. The decoding paradigms are all derived and analysed in a self-contained manner, often in new ways or examined in greater depth than previously. Among a number of new results, we...
Decoding Delay Controlled Completion Time Reduction in Instantly Decodable Network Coding
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.
Decoding Delay Controlled Completion Time Reduction in Instantly Decodable Network Coding
Douik, Ahmed S.; Sorour, Sameh; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim
2016-01-01
For several years, the completion time and the decoding delay problems in Instantly Decodable Network Coding (IDNC) were considered separately and were thought to 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.
Computational methods to dissect cis-regulatory transcriptional ...
Indian Academy of Sciences (India)
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 ...
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...... decoders perform repeated decoding trials and decoding information is exchanged between them...
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.
Fast decoders for qudit topological codes
International Nuclear Information System (INIS)
Anwar, Hussain; Brown, Benjamin J; Campbell, Earl T; Browne, Dan E
2014-01-01
Qudit toric codes are a natural higher-dimensional generalization of the well-studied qubit toric code. However, standard methods for error correction of the qubit toric code are not applicable to them. Novel decoders are needed. In this paper we introduce two renormalization group decoders for qudit codes and analyse their error correction thresholds and efficiency. The first decoder is a generalization of a ‘hard-decisions’ decoder due to Bravyi and Haah (arXiv:1112.3252). We modify this decoder to overcome a percolation effect which limits its threshold performance for many-level quantum systems. The second decoder is a generalization of a ‘soft-decisions’ decoder due to Poulin and Duclos-Cianci (2010 Phys. Rev. Lett. 104 050504), with a small cell size to optimize the efficiency of implementation in the high dimensional case. In each case, we estimate thresholds for the uncorrelated bit-flip error model and provide a comparative analysis of the performance of both these approaches to error correction of qudit toric codes. (paper)
Zhang, Xu; Wang, Fengshan; Sheng, Juzheng
2016-06-16
Heparan sulfate (HS) is widely distributed in mammalian tissues in the form of HS proteoglycans, which play essential roles in various physiological and pathological processes. In contrast to the template-guided processes involved in the synthesis of DNA and proteins, HS biosynthesis is not believed to involve a template. However, it appears that the final structure of HS chains was strictly regulated. Herein, we report research based hypothesis that two major steps, namely "coding" and "decoding" steps, are involved in the biosynthesis of HS, which strictly regulate its chemical structure and biological activity. The "coding" process in this context is based on the distribution of sulfate moieties on the amino groups of the glucosamine residues in the HS chains. The sulfation of these amine groups is catalyzed by N-deacetylase/N-sulfotransferase, which has four isozymes. The composition and distribution of sulfate groups and iduronic acid residues on the glycan chains of HS are determined by several other modification enzymes, which can recognize these coding sequences (i.e., the "decoding" process). The degree and pattern of the sulfation and epimerization in the HS chains determines the extent of their interactions with several different protein factors, which further influences their biological activity. Copyright © 2016 Elsevier Ltd. All rights reserved.
2010-01-01
... 10 Energy 1 2010-01-01 2010-01-01 false Discovery. 13.21 Section 13.21 Energy NUCLEAR REGULATORY COMMISSION PROGRAM FRAUD CIVIL REMEDIES § 13.21 Discovery. (a) The following types of discovery are...) Unless mutually agreed to by the parties, discovery is available only as ordered by the ALJ. The ALJ...
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.
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 al...
Fast decoding algorithms for geometric coded apertures
International Nuclear Information System (INIS)
Byard, Kevin
2015-01-01
Fast decoding algorithms are described for the class of coded aperture designs known as geometric coded apertures which were introduced by Gourlay and Stephen. When compared to the direct decoding method, the algorithms significantly reduce the number of calculations required when performing the decoding for these apertures and hence speed up the decoding process. Experimental tests confirm the efficacy of these fast algorithms, demonstrating a speed up of approximately two to three orders of magnitude over direct decoding.
FPGA implementation of low complexity LDPC iterative decoder
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.
Bounded-Angle Iterative Decoding of LDPC Codes
Dolinar, Samuel; Andrews, Kenneth; Pollara, Fabrizio; Divsalar, Dariush
2009-01-01
Bounded-angle iterative decoding is a modified version of conventional iterative decoding, conceived as a means of reducing undetected-error rates for short low-density parity-check (LDPC) codes. For a given code, bounded-angle iterative decoding can be implemented by means of a simple modification of the decoder algorithm, without redesigning the code. Bounded-angle iterative decoding is based on a representation of received words and code words as vectors in an n-dimensional Euclidean space (where n is an integer).
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...
Pocock, Ginger M; Zimdars, Laraine L; Yuan, Ming; Eliceiri, Kevin W; Ahlquist, Paul; Sherer, Nathan M
2017-02-01
Cis-acting RNA structural elements govern crucial aspects of viral gene expression. How these structures and other posttranscriptional signals affect RNA trafficking and translation in the context of single cells is poorly understood. Herein we describe a multicolor, long-term (>24 h) imaging strategy for measuring integrated aspects of viral RNA regulatory control in individual cells. We apply this strategy to demonstrate differential mRNA trafficking behaviors governed by RNA elements derived from three retroviruses (HIV-1, murine leukemia virus, and Mason-Pfizer monkey virus), two hepadnaviruses (hepatitis B virus and woodchuck hepatitis virus), and an intron-retaining transcript encoded by the cellular NXF1 gene. Striking behaviors include "burst" RNA nuclear export dynamics regulated by HIV-1's Rev response element and the viral Rev protein; transient aggregations of RNAs into discrete foci at or near the nuclear membrane triggered by multiple elements; and a novel, pulsiform RNA export activity regulated by the hepadnaviral posttranscriptional regulatory element. We incorporate single-cell tracking and a data-mining algorithm into our approach to obtain RNA element-specific, high-resolution gene expression signatures. Together these imaging assays constitute a tractable, systems-based platform for studying otherwise difficult to access spatiotemporal features of viral and cellular gene regulation. © 2017 Pocock et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).
The architecture of gene regulatory variation across multiple human tissues: the MuTHER study.
Directory of Open Access Journals (Sweden)
Alexandra C Nica
2011-02-01
Full Text Available While there have been studies exploring regulatory variation in one or more tissues, the complexity of tissue-specificity in multiple primary tissues is not yet well understood. We explore in depth the role of cis-regulatory variation in three human tissues: lymphoblastoid cell lines (LCL, skin, and fat. The samples (156 LCL, 160 skin, 166 fat were derived simultaneously from a subset of well-phenotyped healthy female twins of the MuTHER resource. We discover an abundance of cis-eQTLs in each tissue similar to previous estimates (858 or 4.7% of genes. In addition, we apply factor analysis (FA to remove effects of latent variables, thus more than doubling the number of our discoveries (1,822 eQTL genes. The unique study design (Matched Co-Twin Analysis--MCTA permits immediate replication of eQTLs using co-twins (93%-98% and validation of the considerable gain in eQTL discovery after FA correction. We highlight the challenges of comparing eQTLs between tissues. After verifying previous significance threshold-based estimates of tissue-specificity, we show their limitations given their dependency on statistical power. We propose that continuous estimates of the proportion of tissue-shared signals and direct comparison of the magnitude of effect on the fold change in expression are essential properties that jointly provide a biologically realistic view of tissue-specificity. Under this framework we demonstrate that 30% of eQTLs are shared among the three tissues studied, while another 29% appear exclusively tissue-specific. However, even among the shared eQTLs, a substantial proportion (10%-20% have significant differences in the magnitude of fold change between genotypic classes across tissues. Our results underline the need to account for the complexity of eQTL tissue-specificity in an effort to assess consequences of such variants for complex traits.
Directory of Open Access Journals (Sweden)
Xiaodong Cai
Full Text Available Integrating genetic perturbations with gene expression data not only improves accuracy of regulatory network topology inference, but also enables learning of causal regulatory relations between genes. Although a number of methods have been developed to integrate both types of data, the desiderata of efficient and powerful algorithms still remains. In this paper, sparse structural equation models (SEMs are employed to integrate both gene expression data and cis-expression quantitative trait loci (cis-eQTL, for modeling gene regulatory networks in accordance with biological evidence about genes regulating or being regulated by a small number of genes. A systematic inference method named sparsity-aware maximum likelihood (SML is developed for SEM estimation. Using simulated directed acyclic or cyclic networks, the SML performance is compared with that of two state-of-the-art algorithms: the adaptive Lasso (AL based scheme, and the QTL-directed dependency graph (QDG method. Computer simulations demonstrate that the novel SML algorithm offers significantly better performance than the AL-based and QDG algorithms across all sample sizes from 100 to 1,000, in terms of detection power and false discovery rate, in all the cases tested that include acyclic or cyclic networks of 10, 30 and 300 genes. The SML method is further applied to infer a network of 39 human genes that are related to the immune function and are chosen to have a reliable eQTL per gene. The resulting network consists of 9 genes and 13 edges. Most of the edges represent interactions reasonably expected from experimental evidence, while the remaining may just indicate the emergence of new interactions. The sparse SEM and efficient SML algorithm provide an effective means of exploiting both gene expression and perturbation data to infer gene regulatory networks. An open-source computer program implementing the SML algorithm is freely available upon request.
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...
Decoding small surface codes with feedforward neural networks
Varsamopoulos, Savvas; Criger, Ben; Bertels, Koen
2018-01-01
Surface codes reach high error thresholds when decoded with known algorithms, but the decoding time will likely exceed the available time budget, especially for near-term implementations. To decrease the decoding time, we reduce the decoding problem to a classification problem that a feedforward neural network can solve. We investigate quantum error correction and fault tolerance at small code distances using neural network-based decoders, demonstrating that the neural network can generalize to inputs that were not provided during training and that they can reach similar or better decoding performance compared to previous algorithms. We conclude by discussing the time required by a feedforward neural network decoder in hardware.
Evolution of cichlid vision via trans-regulatory divergence
Directory of Open Access Journals (Sweden)
O’Quin Kelly E
2012-12-01
Full Text Available Abstract Background Phenotypic evolution may occur through mutations that affect either the structure or expression of protein-coding genes. Although the evolution of color vision has historically been attributed to structural mutations within the opsin genes, recent research has shown that opsin regulatory mutations can also tune photoreceptor sensitivity and color vision. Visual sensitivity in African cichlid fishes varies as a result of the differential expression of seven opsin genes. We crossed cichlid species that express different opsin gene sets and scanned their genome for expression Quantitative Trait Loci (eQTL responsible for these differences. Our results shed light on the role that different structural, cis-, and trans-regulatory mutations play in the evolution of color vision. Results We identified 11 eQTL that contribute to the divergent expression of five opsin genes. On three linkage groups, several eQTL formed regulatory “hotspots” associated with the expression of multiple opsins. Importantly, however, the majority of the eQTL we identified (8/11 or 73% occur on linkage groups located trans to the opsin genes, suggesting that cichlid color vision has evolved primarily via trans-regulatory divergence. By modeling the impact of just two of these trans-regulatory eQTL, we show that opsin regulatory mutations can alter cichlid photoreceptor sensitivity and color vision at least as much as opsin structural mutations can. Conclusions Combined with previous work, we demonstrate that the evolution of cichlid color vision results from the interplay of structural, cis-, and especially trans-regulatory loci. Although there are numerous examples of structural and cis-regulatory mutations that contribute to phenotypic evolution, our results suggest that trans-regulatory mutations could contribute to phenotypic divergence more commonly than previously expected, especially in systems like color vision, where compensatory changes in the
Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers
Directory of Open Access Journals (Sweden)
Parker Hugo J
2011-12-01
Full Text Available Abstract Background Gene regulation through cis-regulatory elements plays a crucial role in development and disease. A major aim of the post-genomic era is to be able to read the function of cis-regulatory elements through scrutiny of their DNA sequence. Whilst comparative genomics approaches have identified thousands of putative regulatory elements, our knowledge of their mechanism of action is poor and very little progress has been made in systematically de-coding them. Results Here, we identify ancient functional signatures within vertebrate conserved non-coding elements (CNEs through a combination of phylogenetic footprinting and functional assay, using genomic sequence from the sea lamprey as a reference. We uncover a striking enrichment within vertebrate CNEs for conserved binding-site motifs of the Pbx-Hox hetero-dimer. We further show that these predict reporter gene expression in a segment specific manner in the hindbrain and pharyngeal arches during zebrafish development. Conclusions These findings evoke an evolutionary scenario in which many CNEs evolved early in the vertebrate lineage to co-ordinate Hox-dependent gene-regulatory interactions that pattern the vertebrate head. In a broader context, our evolutionary analyses reveal that CNEs are composed of tightly linked transcription-factor binding-sites (TFBSs, which can be systematically identified through phylogenetic footprinting approaches. By placing a large number of ancient vertebrate CNEs into a developmental context, our findings promise to have a significant impact on efforts toward de-coding gene-regulatory elements that underlie vertebrate development, and will facilitate building general models of regulatory element evolution.
Video coding for decoding power-constrained embedded devices
Lu, Ligang; Sheinin, Vadim
2004-01-01
Low power dissipation and fast processing time are crucial requirements for embedded multimedia devices. This paper presents a technique in video coding to decrease the power consumption at a standard video decoder. Coupled with a small dedicated video internal memory cache on a decoder, the technique can substantially decrease the amount of data traffic to the external memory at the decoder. A decrease in data traffic to the external memory at decoder will result in multiple benefits: faster real-time processing and power savings. The encoder, given prior knowledge of the decoder"s dedicated video internal memory cache management scheme, regulates its choice of motion compensated predictors to reduce the decoder"s external memory accesses. This technique can be used in any standard or proprietary encoder scheme to generate a compliant output bit stream decodable by standard CPU-based and dedicated hardware-based decoders for power savings with the best quality-power cost trade off. Our simulation results show that with a relatively small amount of dedicated video internal memory cache, the technique may decrease the traffic between CPU and external memory over 50%.
A novel parallel pipeline structure of VP9 decoder
Qin, Huabiao; Chen, Wu; Yi, Sijun; Tan, Yunfei; Yi, Huan
2018-04-01
To improve the efficiency of VP9 decoder, a novel parallel pipeline structure of VP9 decoder is presented in this paper. According to the decoding workflow, VP9 decoder can be divided into sub-modules which include entropy decoding, inverse quantization, inverse transform, intra prediction, inter prediction, deblocking and pixel adaptive compensation. By analyzing the computing time of each module, hotspot modules are located and the causes of low efficiency of VP9 decoder can be found. Then, a novel pipeline decoder structure is designed by using mixed parallel decoding methods of data division and function division. The experimental results show that this structure can greatly improve the decoding efficiency of VP9.
SYMBOL LEVEL DECODING FOR DUO-BINARY TURBO CODES
Directory of Open Access Journals (Sweden)
Yogesh Beeharry
2017-05-01
Full Text Available This paper investigates the performance of three different symbol level decoding algorithms for Duo-Binary Turbo codes. Explicit details of the computations involved in the three decoding techniques, and a computational complexity analysis are given. Simulation results with different couple lengths, code-rates, and QPSK modulation reveal that the symbol level decoding with bit-level information outperforms the symbol level decoding by 0.1 dB on average in the error floor region. Moreover, a complexity analysis reveals that symbol level decoding with bit-level information reduces the decoding complexity by 19.6 % in terms of the total number of computations required for each half-iteration as compared to symbol level decoding.
Energy Technology Data Exchange (ETDEWEB)
Sakai, A.; Fedorov, A; Fedorov, E; Schnoes, A; Glasner, M; Burley, S; Babbitt, P; Almo, S; Gerlt, J
2009-01-01
The mechanistically diverse enolase superfamily is a paradigm for elucidating Nature's strategies for divergent evolution of enzyme function. Each of the different reactions catalyzed by members of the superfamily is initiated by abstraction of the a-proton of a carboxylate substrate that is coordinated to an essential Mg2+. The muconate lactonizing enzyme (MLE) from Pseudomonas putida, a member of a family that catalyzes the syn-cycloisomerization of cis,cis-muconate to (4S)-muconolactone in the e-ketoadipate pathway, has provided critical insights into the structural bases for evolution of function within the superfamily. A second, divergent family of homologous MLEs that catalyzes anti-cycloisomerization has been identified. Structures of members of both families liganded with the common (4S)-muconolactone product (syn, Pseudomonas fluorescens, gi 70731221; anti, Mycobacterium smegmatis, gi 118470554) document that the conserved Lys at the end of the second e-strand in the (e/a)7e-barrel domain serves as the acid catalyst in both reactions. The different stereochemical courses (syn and anti) result from different structural strategies for determining substrate specificity: although the distal carboxylate group of the cis,cis-muconate substrate attacks the same face of the proximal double bond, opposite faces of the resulting enolate anion intermediate are presented to the conserved Lys acid catalyst. The discovery of two families of homologous, but stereochemically distinct, MLEs likely provides an example of 'pseudoconvergent' evolution of the same function from different homologous progenitors within the enolase superfamily, in which different spatial arrangements of active site functional groups and substrate specificity determinants support catalysis of the same reaction.
Sakai, Ayano; Fedorov, Alexander A.; Fedorov, Elena V.; Schnoes, Alexandra M.; Glasner, Margaret E.; Brown, Shoshana; Rutter, Marc E.; Bain, Kevin; Chang, Shawn; Gheyi, Tarun; Sauder, J. Michael; Burley, Stephen K.; Babbitt, Patricia C.; Almo, Steven C.; Gerlt, John A.
2009-01-01
The mechanistically diverse enolase superfamily is a paradigm for elucidating Nature’s strategies for divergent evolution of enzyme function. Each of the different reactions catalyzed by members of the superfamily is initiated by abstraction of the α-proton of a carboxylate substrate that is coordinated to an essential Mg2+. The muconate lactonizing enzyme (MLE) from Pseudomonas putida, a member of a family that catalyzes the syn-cycloisomerization of cis,cis-muconate to (4S)-muconolactone in the β-ketoadipate pathway, has provided critical insights into the structural bases for evolution of function within the superfamily. A second, divergent family of homologues MLEs that catalyzes anti-cycloisomerization has been identified. Structures of members of both families liganded with the common (4S)-muconolactone product (syn, Pseudomonas fluorescens, GI:70731221; anti, Mycobacterium smegmatis, GI:118470554) document that the conserved Lys at the end of the second β-strand in the (β/α)7β-barrel domain serves as the acid catalyst in both reactions. The different stereochemical courses (syn and anti) result from different structural strategies for determining substrate specificity: although the distal carboxylate group of the cis,cis-muconate substrate attacks the same face of the proximal double bond, opposite faces of the resulting enolate anion intermediate are presented to the conserved Lys acid catalyst. The discovery of two families of homologous, but stereochemically distinct, MLEs likely provides an example of “pseudoconvergent” evolution of the same function from different homologous progenitors within the enolase superfamily, in which different spatial arrangements of active site functional groups and substrate specificity determinants support catalysis of the same reaction. PMID:19220063
2010-01-01
... 10 Energy 1 2010-01-01 2010-01-01 false Discovery. 2.1018 Section 2.1018 Energy NUCLEAR REGULATORY... Geologic Repository § 2.1018 Discovery. (a)(1) Parties, potential parties, and interested governmental participants in the high-level waste licensing proceeding may obtain discovery by one or more of the following...
NP-hardness of decoding quantum error-correction codes
Hsieh, Min-Hsiu; Le Gall, François
2011-05-01
Although the theory of quantum error correction is intimately related to classical coding theory and, in particular, one can construct quantum error-correction codes (QECCs) from classical codes with the dual-containing property, this does not necessarily imply that the computational complexity of decoding QECCs is the same as their classical counterparts. Instead, decoding QECCs can be very much different from decoding classical codes due to the degeneracy property. Intuitively, one expects degeneracy would simplify the decoding since two different errors might not and need not be distinguished in order to correct them. However, we show that general quantum decoding problem is NP-hard regardless of the quantum codes being degenerate or nondegenerate. This finding implies that no considerably fast decoding algorithm exists for the general quantum decoding problems and suggests the existence of a quantum cryptosystem based on the hardness of decoding QECCs.
NP-hardness of decoding quantum error-correction codes
International Nuclear Information System (INIS)
Hsieh, Min-Hsiu; Le Gall, Francois
2011-01-01
Although the theory of quantum error correction is intimately related to classical coding theory and, in particular, one can construct quantum error-correction codes (QECCs) from classical codes with the dual-containing property, this does not necessarily imply that the computational complexity of decoding QECCs is the same as their classical counterparts. Instead, decoding QECCs can be very much different from decoding classical codes due to the degeneracy property. Intuitively, one expects degeneracy would simplify the decoding since two different errors might not and need not be distinguished in order to correct them. However, we show that general quantum decoding problem is NP-hard regardless of the quantum codes being degenerate or nondegenerate. This finding implies that no considerably fast decoding algorithm exists for the general quantum decoding problems and suggests the existence of a quantum cryptosystem based on the hardness of decoding QECCs.
Evaluation framework for K-best sphere decoders
Shen, Chungan; Eltawil, Ahmed M.; Salama, Khaled N.
2010-01-01
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
Neural Decoder for Topological Codes
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.
Rokytskyy, Ihor; Koshla, Oksana; Fedorenko, Victor; Ostash, Bohdan
2016-01-01
The gene bldA for leucyl [Formula: see text] is known for almost 30 years as a key regulator of morphogenesis and secondary metabolism in genus Streptomyces. Codon UUA is the rarest one in Streptomyces genomes and is present exclusively in genes with auxiliary functions. Delayed accumulation of translation-competent [Formula: see text] is believed to confine the expression of UUA-containing transcripts to stationary phase. Implicit to the regulatory function of UUA codon is the assumption about high accuracy of its translation, e.g. the latter should not occur in the absence of cognate [Formula: see text]. However, a growing body of facts points to the possibility of mistranslation of UUA-containing transcripts in the bldA-deficient mutants. It is not known what type of near-cognate tRNA(s) may decode UUA in the absence of cognate tRNA in Streptomyces, and whether UUA possesses certain inherent properties (such as increased/decreased accuracy of decoding) that would favor its use for regulatory purposes. Here we took bioinformatic approach to address these questions. We catalogued the entire complement of tRNA genes from several relevant Streptomyces and identified genes for posttranscriptional modifications of tRNA that might be involved in UUA decoding by cognate and near-cognate tRNAs. Based on tRNA gene content in Streptomyces genomes, we propose possible scenarios of UUA codon mistranslation. UUA is not associated with an increased rate of missense errors as compared to other leucyl codons, contrasting general belief that low-abundant codons are more error-prone than the high-abundant ones.
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.
The serial message-passing schedule for LDPC decoding algorithms
Liu, Mingshan; Liu, Shanshan; Zhou, Yuan; Jiang, Xue
2015-12-01
The conventional message-passing schedule for LDPC decoding algorithms is the so-called flooding schedule. It has the disadvantage that the updated messages cannot be used until next iteration, thus reducing the convergence speed . In this case, the Layered Decoding algorithm (LBP) based on serial message-passing schedule is proposed. In this paper the decoding principle of LBP algorithm is briefly introduced, and then proposed its two improved algorithms, the grouped serial decoding algorithm (Grouped LBP) and the semi-serial decoding algorithm .They can improve LBP algorithm's decoding speed while maintaining a good decoding performance.
Directory of Open Access Journals (Sweden)
Iraê A. Guerrini
2005-01-01
Full Text Available Abscisic acid (ABA regulates stress responses in plants, and genomic tools can help us to understand the mechanisms involved in that process. FAPESP, a Brazilian research foundation, in association with four private forestry companies, has established the FORESTs database (https://forests.esalq.usp.br. A search was carried out in the Eucalyptus expressed sequence tag database to find ESTs involved with 9-cis epoxycarotenoid dioxygenase (NCED, the regulatory enzyme for ABA biosynthesis, using the basic local BLAST alignment tool. We found four clusters (EGEZLV2206B11.g, EGJMWD2252H08.g, EGBFRT3107F10.g, and EGEQFB1200H10.g, which represent similar sequences of the gene that produces NCED. Data showed that the EGBFRT3107F10.g cluster was similar to the maize (Zea mays NCED enzyme, while EGEZLV2206B11.g and EGJMWD2252H08.g clusters were similar to the avocado (Persea americana NCED enzyme. All Eucalyptus clusters were expressed in several tissues, especially in flower buds, where ABA has a special participation during the floral development process.
Improved Power Decoding of One-Point Hermitian Codes
DEFF Research Database (Denmark)
Puchinger, Sven; Bouw, Irene; Rosenkilde, Johan Sebastian Heesemann
2017-01-01
We propose a new partial decoding algorithm for one-point Hermitian codes that can decode up to the same number of errors as the Guruswami–Sudan decoder. Simulations suggest that it has a similar failure probability as the latter one. The algorithm is based on a recent generalization of the power...... decoding algorithm for Reed–Solomon codes and does not require an expensive root-finding step. In addition, it promises improvements for decoding interleaved Hermitian codes....
Decoding communities in networks.
Radicchi, Filippo
2018-02-01
According to a recent information-theoretical proposal, the problem of defining and identifying communities in networks can be interpreted as a classical communication task over a noisy channel: memberships of nodes are information bits erased by the channel, edges and nonedges in the network are parity bits introduced by the encoder but degraded through the channel, and a community identification algorithm is a decoder. The interpretation is perfectly equivalent to the one at the basis of well-known statistical inference algorithms for community detection. The only difference in the interpretation is that a noisy channel replaces a stochastic network model. However, the different perspective gives the opportunity to take advantage of the rich set of tools of coding theory to generate novel insights on the problem of community detection. In this paper, we illustrate two main applications of standard coding-theoretical methods to community detection. First, we leverage a state-of-the-art decoding technique to generate a family of quasioptimal community detection algorithms. Second and more important, we show that the Shannon's noisy-channel coding theorem can be invoked to establish a lower bound, here named as decodability bound, for the maximum amount of noise tolerable by an ideal decoder to achieve perfect detection of communities. When computed for well-established synthetic benchmarks, the decodability bound explains accurately the performance achieved by the best community detection algorithms existing on the market, telling us that only little room for their improvement is still potentially left.
Decoding communities in networks
Radicchi, Filippo
2018-02-01
According to a recent information-theoretical proposal, the problem of defining and identifying communities in networks can be interpreted as a classical communication task over a noisy channel: memberships of nodes are information bits erased by the channel, edges and nonedges in the network are parity bits introduced by the encoder but degraded through the channel, and a community identification algorithm is a decoder. The interpretation is perfectly equivalent to the one at the basis of well-known statistical inference algorithms for community detection. The only difference in the interpretation is that a noisy channel replaces a stochastic network model. However, the different perspective gives the opportunity to take advantage of the rich set of tools of coding theory to generate novel insights on the problem of community detection. In this paper, we illustrate two main applications of standard coding-theoretical methods to community detection. First, we leverage a state-of-the-art decoding technique to generate a family of quasioptimal community detection algorithms. Second and more important, we show that the Shannon's noisy-channel coding theorem can be invoked to establish a lower bound, here named as decodability bound, for the maximum amount of noise tolerable by an ideal decoder to achieve perfect detection of communities. When computed for well-established synthetic benchmarks, the decodability bound explains accurately the performance achieved by the best community detection algorithms existing on the market, telling us that only little room for their improvement is still potentially left.
DEFF Research Database (Denmark)
Andersen, Mads Hald
2017-01-01
responses to tumours or inhibiting autoimmunity development. However, recent studies report the discovery of self-reactive pro-inflammatory T cells—termed anti-regulatory T cells (anti-Tregs)—that target immune-suppressive cells. Thus, regulatory cells can now be defined as both cells that suppress immune...... reactions as well as effector cells that counteract the effects of suppressor cells and support immune reactions. Self-reactive anti-Tregs have been described that specifically recognize human leukocyte antigen-restricted epitopes derived from proteins that are normally expressed by regulatory immune cells......Our initial understanding of immune-regulatory cells was based on the discovery of suppressor cells that assure peripheral T-cell tolerance and promote immune homeostasis. Research has particularly focused on the importance of regulatory T cells (Tregs) for immune modulation, e.g. directing host...
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
On Lattice Sequential Decoding for The Unconstrained AWGN Channel
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.
On Lattice Sequential Decoding for The Unconstrained AWGN Channel
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.
On Lattice Sequential Decoding for The Unconstrained AWGN Channel
Abediseid, Walid; Alouini, Mohamed-Slim
2012-01-01
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.
Interior point decoding for linear vector channels
International Nuclear Information System (INIS)
Wadayama, T
2008-01-01
In this paper, a novel decoding algorithm for low-density parity-check (LDPC) codes based on convex optimization is presented. The decoding algorithm, called interior point decoding, is designed for linear vector channels. The linear vector channels include many practically important channels such as inter-symbol interference channels and partial response channels. It is shown that the maximum likelihood decoding (MLD) rule for a linear vector channel can be relaxed to a convex optimization problem, which is called a relaxed MLD problem
Interior point decoding for linear vector channels
Energy Technology Data Exchange (ETDEWEB)
Wadayama, T [Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, Aichi, 466-8555 (Japan)], E-mail: wadayama@nitech.ac.jp
2008-01-15
In this paper, a novel decoding algorithm for low-density parity-check (LDPC) codes based on convex optimization is presented. The decoding algorithm, called interior point decoding, is designed for linear vector channels. The linear vector channels include many practically important channels such as inter-symbol interference channels and partial response channels. It is shown that the maximum likelihood decoding (MLD) rule for a linear vector channel can be relaxed to a convex optimization problem, which is called a relaxed MLD problem.
Symbol synchronization for the TDRSS decoder
Costello, D. J., Jr.
1983-01-01
Each 8 bits out of the Viterbi decoder correspond to one symbol of the R/S code. Synchronization must be maintained here so that each 8-bit symbol delivered to the R/S decoder corresponds to an 8-bit symbol from the R/S encoder. Lack of synchronization, would cause an error in almost every R/S symbol since even a - 1-bit sync slip shifts every bit in each 8-bit symbol by one position, therby confusing the mapping betweeen 8-bit sequences and symbols. The error correcting capability of the R/S code would be exceeded. Possible ways to correcting this condition include: (1) designing the R/S decoder to recognize the overload and shifting the output sequence of the inner decoder to establish a different sync state; (2) using the characteristics of the inner decoder to establish symbol synchronization for the outer code, with or without a deinterleaver and an interleaver; and (3) modifying the encoder to alternate periodically between two sets of generators.
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....
Multi-stage decoding for multi-level block modulation codes
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.
Kazemian, Majid; Suryamohan, Kushal; Chen, Jia-Yu; Zhang, Yinan; Samee, Md Abul Hassan; Halfon, Marc S; Sinha, Saurabh
2014-09-01
Many genes familiar from Drosophila development, such as the so-called gap, pair-rule, and segment polarity genes, play important roles in the development of other insects and in many cases appear to be deployed in a similar fashion, despite the fact that Drosophila-like "long germband" development is highly derived and confined to a subset of insect families. Whether or not these similarities extend to the regulatory level is unknown. Identification of regulatory regions beyond the well-studied Drosophila has been challenging as even within the Diptera (flies, including mosquitoes) regulatory sequences have diverged past the point of recognition by standard alignment methods. Here, we demonstrate that methods we previously developed for computational cis-regulatory module (CRM) discovery in Drosophila can be used effectively in highly diverged (250-350 Myr) insect species including Anopheles gambiae, Tribolium castaneum, Apis mellifera, and Nasonia vitripennis. In Drosophila, we have successfully used small sets of known CRMs as "training data" to guide the search for other CRMs with related function. We show here that although species-specific CRM training data do not exist, training sets from Drosophila can facilitate CRM discovery in diverged insects. We validate in vivo over a dozen new CRMs, roughly doubling the number of known CRMs in the four non-Drosophila species. Given the growing wealth of Drosophila CRM annotation, these results suggest that extensive regulatory sequence annotation will be possible in newly sequenced insects without recourse to costly and labor-intensive genome-scale experiments. We develop a new method, Regulus, which computes a probabilistic score of similarity based on binding site composition (despite the absence of nucleotide-level sequence alignment), and demonstrate similarity between functionally related CRMs from orthologous loci. Our work represents an important step toward being able to trace the evolutionary history of gene
Zhang, Yinan; Samee, Md. Abul Hassan; Halfon, Marc S.; Sinha, Saurabh
2014-01-01
Many genes familiar from Drosophila development, such as the so-called gap, pair-rule, and segment polarity genes, play important roles in the development of other insects and in many cases appear to be deployed in a similar fashion, despite the fact that Drosophila-like “long germband” development is highly derived and confined to a subset of insect families. Whether or not these similarities extend to the regulatory level is unknown. Identification of regulatory regions beyond the well-studied Drosophila has been challenging as even within the Diptera (flies, including mosquitoes) regulatory sequences have diverged past the point of recognition by standard alignment methods. Here, we demonstrate that methods we previously developed for computational cis-regulatory module (CRM) discovery in Drosophila can be used effectively in highly diverged (250–350 Myr) insect species including Anopheles gambiae, Tribolium castaneum, Apis mellifera, and Nasonia vitripennis. In Drosophila, we have successfully used small sets of known CRMs as “training data” to guide the search for other CRMs with related function. We show here that although species-specific CRM training data do not exist, training sets from Drosophila can facilitate CRM discovery in diverged insects. We validate in vivo over a dozen new CRMs, roughly doubling the number of known CRMs in the four non-Drosophila species. Given the growing wealth of Drosophila CRM annotation, these results suggest that extensive regulatory sequence annotation will be possible in newly sequenced insects without recourse to costly and labor-intensive genome-scale experiments. We develop a new method, Regulus, which computes a probabilistic score of similarity based on binding site composition (despite the absence of nucleotide-level sequence alignment), and demonstrate similarity between functionally related CRMs from orthologous loci. Our work represents an important step toward being able to trace the evolutionary
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 gi...... and a duality in the choice of parameters needed for decoding, both in the case of GRS codes and in the case of Goppa codes....
Energy Technology Data Exchange (ETDEWEB)
Hong, R. L., Hamaguchi, L., Busch, M. A., and Weigel, D.
2003-06-01
OAK-B135 In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3 kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for activity of AG regulatory sequences in A. thaliana. Although there is little obvious sequence similarity outside the Brassicaceae, the intron from cucumber AG has at least partial activity in A. thaliana. Our studies underscore the value of the comparative approach as a tool that complements gene-by-gene promoter dissection, but also highlight that sequence-based studies alone are insufficient for a complete identification of cis-regulatory sites.
Small RNAs and the regulation of cis-natural antisense transcripts in Arabidopsis
Directory of Open Access Journals (Sweden)
Lonardi Stefano
2008-01-01
mitochondrion-targeted proteins are over-represented in the Arabidopsis cis-NATs and that 19% of sense and antisense partner genes of cis-NATs share at least one common Gene Ontology term, which suggests that they encode proteins with possible functional connection. Conclusion The negatively correlated expression patterns of sense and antisense genes as well as the presence of siRNAs in many of the cis-NATs suggest that siRNA regulation of cis-NATs via the RNAi pathway is an important gene regulatory mechanism for at least a subgroup of cis-NATs in Arabidopsis.
Pierce, Brandon L.; Tong, Lin; Chen, Lin S.; Rahaman, Ronald; Argos, Maria; Jasmine, Farzana; Roy, Shantanu; Paul-Brutus, Rachelle; Westra, Harm-Jan; Franke, Lude; Esko, Tonu; Zaman, Rakibuz; Islam, Tariqul; Rahman, Mahfuzar; Baron, John A.; Kibriya, Muhammad G.; Ahsan, Habibul
2014-01-01
A large fraction of human genes are regulated by genetic variation near the transcribed sequence (cis-eQTL, expression quantitative trait locus), and many cis-eQTLs have implications for human disease. Less is known regarding the effects of genetic variation on expression of distant genes (trans-eQTLs) and their biological mechanisms. In this work, we use genome-wide data on SNPs and array-based expression measures from mononuclear cells obtained from a population-based cohort of 1,799 Bangladeshi individuals to characterize cis- and trans-eQTLs and determine if observed trans-eQTL associations are mediated by expression of transcripts in cis with the SNPs showing trans-association, using Sobel tests of mediation. We observed 434 independent trans-eQTL associations at a false-discovery rate of 0.05, and 189 of these trans-eQTLs were also cis-eQTLs (enrichment Pmediator based on Sobel Pmediation signals in two European cohorts, and while only 7 trans-eQTL associations were present in one or both cohorts, 6 showed evidence of cis-mediation. Analyses of simulated data show that complete mediation will be observed as partial mediation in the presence of mediator measurement error or imperfect LD between measured and causal variants. Our data demonstrates that trans-associations can become significantly stronger or switch directions after adjusting for a potential mediator. Using simulated data, we demonstrate that this phenomenon is expected in the presence of strong cis-trans confounding and when the measured cis-transcript is correlated with the true (unmeasured) mediator. In conclusion, by applying mediation analysis to eQTL data, we show that a substantial fraction of observed trans-eQTL associations can be explained by cis-mediation. Future studies should focus on understanding the mechanisms underlying widespread cis-mediation and their relevance to disease biology, as well as using mediation analysis to improve eQTL discovery. PMID:25474530
Encoder-decoder optimization for brain-computer interfaces.
Merel, Josh; Pianto, Donald M; Cunningham, John P; Paninski, Liam
2015-06-01
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.
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.
Iterative Decoding of Concatenated Codes: A Tutorial
Directory of Open Access Journals (Sweden)
Phillip A. Regalia
2005-05-01
Full Text Available The turbo decoding algorithm of a decade ago constituted a milestone in error-correction coding for digital communications, and has inspired extensions to generalized receiver topologies, including turbo equalization, turbo synchronization, and turbo CDMA, among others. Despite an accrued understanding of iterative decoding over the years, the “turbo principle†remains elusive to master analytically, thereby inciting interest from researchers outside the communications domain. In this spirit, we develop a tutorial presentation of iterative decoding for parallel and serial concatenated codes, in terms hopefully accessible to a broader audience. We motivate iterative decoding as a computationally tractable attempt to approach maximum-likelihood decoding, and characterize fixed points in terms of a “consensus†property between constituent decoders. We review how the decoding algorithm for both parallel and serial concatenated codes coincides with an alternating projection algorithm, which allows one to identify conditions under which the algorithm indeed converges to a maximum-likelihood solution, in terms of particular likelihood functions factoring into the product of their marginals. The presentation emphasizes a common framework applicable to both parallel and serial concatenated codes.
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.
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.
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...
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...... 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...... and various other functions needed in a complete system is presented. Two such units are described, one for placement before the Viterbi decoder and another for placement after the decoder. The high level architectures of three possible implementations of Viterbi decoders are described: The first...
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...... 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...... towards a realization in an FPGA.Node synchronization performed within a Viterbi decoder is discussed, and the high level architectures of three possible implementations of Viterbi decoders are described: The first implementation uses a number of commercially available decoders while the the two others...
A Scalable Architecture of a Structured LDPC Decoder
Lee, Jason Kwok-San; Lee, Benjamin; Thorpe, Jeremy; Andrews, Kenneth; Dolinar, Sam; Hamkins, Jon
2004-01-01
We present a scalable decoding architecture for a certain class of structured LDPC codes. The codes are designed using a small (n,r) protograph that is replicated Z times to produce a decoding graph for a (Z x n, Z x r) code. Using this architecture, we have implemented a decoder for a (4096,2048) LDPC code on a Xilinx Virtex-II 2000 FPGA, and achieved decoding speeds of 31 Mbps with 10 fixed iterations. The implemented message-passing algorithm uses an optimized 3-bit non-uniform quantizer that operates with 0.2dB implementation loss relative to a floating point decoder.
Ancient and recent positive selection transformed opioid cis-regulation in humans.
Directory of Open Access Journals (Sweden)
Matthew V Rockman
2005-12-01
Full Text Available Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking. We found that positive natural selection altered the cis-regulation of human prodynorphin, the precursor molecule for a suite of endogenous opioids and neuropeptides with critical roles in regulating perception, behavior, and memory. Independent lines of phylogenetic and population genetic evidence support a history of selective sweeps driving the evolution of the human prodynorphin promoter. In experimental assays of chimpanzee-human hybrid promoters, the selected sequence increases transcriptional inducibility. The evidence for a change in the response of the brain's natural opioids to inductive stimuli points to potential human-specific characteristics favored during evolution. In addition, the pattern of linked nucleotide and microsatellite variation among and within modern human populations suggests that recent selection, subsequent to the fixation of the human-specific mutations and the peopling of the globe, has favored different prodynorphin cis-regulatory alleles in different parts of the world.
Evaluation framework for K-best sphere decoders
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.
Schippers, I J; Kloppenburg, M; Snippe, L; Ab, G
1994-11-01
The chicken very low density apolipoprotein II (apoVLDLII) gene is estrogen-inducible and specifically expressed in liver. We examined the possible involvement of the retinoid X receptor (RXR) and its ligand 9-cis-retinoic acid (9-cis-RA) in the activation of the apoVLDLII promoter. We first concentrated on a potential RXR recognition site, which deviates at only one position from a perfect direct A/GGGTCA repeat spaced by one nucleotide (DR-1) and was earlier identified as a common HNF-4/COUP-TF recognition site. However, band shift analysis revealed that this imperfect DR-1 motif does not interact with RXR alpha-homodimers. In accordance with this observation we found that this regulatory element does not mediate transactivation through RXR alpha in the presence of 9-cis-RA. However, our experiments revealed another, unexpected, effect of 9-cis-RA. Instead of stimulating, 9-cis-RA attenuated estrogen-induced expression of transfected estrogen-responsive VLDL-CAT reporter plasmids. This repression appeared to take place through the main estrogen response element (ERE) of the gene. Importantly, 9-cis-RA also strongly repressed the estrogen-induced expression of the endogenous apoVLDLII gene in cultured chicken hepatoma cells.
Directory of Open Access Journals (Sweden)
Kristofer Davie
2015-02-01
Full Text Available Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs. When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling
Orientation decoding: Sense in spirals?
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. Copyright © 2014 Elsevier Inc. All rights reserved.
Grasp movement decoding from premotor and parietal cortex.
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.
O2-GIDNC: Beyond instantly decodable network coding
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.
On decoding of multi-level MPSK modulation codes
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.
Multi-stage decoding of multi-level modulation codes
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).
Binary Systematic Network Coding for Progressive Packet Decoding
Jones, Andrew L.; Chatzigeorgiou, Ioannis; Tassi, Andrea
2015-01-01
We consider binary systematic network codes and investigate their capability of decoding a source message either in full or in part. We carry out a probability analysis, derive closed-form expressions for the decoding probability and show that systematic network coding outperforms conventional net- work coding. We also develop an algorithm based on Gaussian elimination that allows progressive decoding of source packets. Simulation results show that the proposed decoding algorithm can achieve ...
Power decoding Reed-Solomon codes up to the Johnson radius
DEFF Research Database (Denmark)
Rosenkilde, Johan Sebastian Heesemann
2018-01-01
Power decoding, or "decoding using virtual interleaving" is a technique for decoding Reed-Solomon codes up to the Sudan radius. Since the method's inception, it has been an open question if it is possible to use this approach to decode up to the Johnson radius - the decoding radius of the Guruswami...
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....
Polar Coding with CRC-Aided List Decoding
2015-08-01
TECHNICAL REPORT 2087 August 2015 Polar Coding with CRC-Aided List Decoding David Wasserman Approved...list decoding . RESULTS Our simulation results show that polar coding can produce results very similar to the FEC used in the Digital Video...standard. RECOMMENDATIONS In any application for which the DVB-S2 FEC is considered, polar coding with CRC-aided list decod - ing with N = 65536
Directory of Open Access Journals (Sweden)
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.
Decoding of concatenated codes with interleaved outer codes
DEFF Research Database (Denmark)
Justesen, Jørn; Høholdt, Tom; Thommesen, Christian
2004-01-01
Recently Bleichenbacher et al. proposed a decoding algorithm for interleaved (N, K) Reed-Solomon codes, which allows close to N-K errors to be corrected in many cases. We discuss the application of this decoding algorithm to concatenated codes.......Recently Bleichenbacher et al. proposed a decoding algorithm for interleaved (N, K) Reed-Solomon codes, which allows close to N-K errors to be corrected in many cases. We discuss the application of this decoding algorithm to concatenated codes....
Image transmission system using adaptive joint source and channel decoding
Liu, Weiliang; Daut, David G.
2005-03-01
In this paper, an adaptive joint source and channel decoding method is designed to accelerate the convergence of the iterative log-dimain 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, which makes 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. Due to the error resilience modes, some bits are known to be either correct or in error. The positions of these bits are then fed back to the channel decoder. The log-likelihood ratios (LLR) 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. That is, for lower channel SNR, a larger factor is assigned, and vice versa. 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 non-source controlled decoding method up to 5dB in terms of PSNR for various reconstructed images.
Iterative channel decoding of FEC-based multiple-description codes.
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.
Modified Decoding Algorithm of LLR-SPA
Directory of Open Access Journals (Sweden)
Zhongxun Wang
2014-09-01
Full Text Available In wireless sensor networks, the energy consumption is mainly occurred in the stage of information transmission. The Low Density Parity Check code can make full use of the channel information to save energy. Because of the widely used decoding algorithm of the Low Density Parity Check code, this paper proposes a new decoding algorithm which is based on the LLR-SPA (Sum-Product Algorithm in Log-Likelihood-domain to improve the accuracy of the decoding algorithm. In the modified algorithm, a piecewise linear function is used to approximate the complicated Jacobi correction term in LLR-SPA decoding algorithm. Construct the tangent by the tangency point to the function of Jacobi correction term, which is based on the first order Taylor Series. In this way, the proposed piecewise linear approximation offers almost a perfect match to the function of Jacobi correction term. Meanwhile, the proposed piecewise linear approximation could avoid the operation of logarithmic which is more suitable for practical application. The simulation results show that the proposed algorithm could improve the decoding accuracy greatly without noticeable variation of the computational complexity.
Real-time minimal-bit-error probability decoding of convolutional codes
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.
Real-time minimal bit error probability decoding of convolutional codes
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.
Cis-regulatory RNA elements that regulate specialized ribosome activity.
Xue, Shifeng; Barna, Maria
2015-01-01
Recent evidence has shown that the ribosome itself can play a highly regulatory role in the specialized translation of specific subpools of mRNAs, in particular at the level of ribosomal proteins (RP). However, the mechanism(s) by which this selection takes place has remained poorly understood. In our recent study, we discovered a combination of unique RNA elements in the 5'UTRs of mRNAs that allows for such control by the ribosome. These mRNAs contain a Translation Inhibitory Element (TIE) that inhibits general cap-dependent translation, and an Internal Ribosome Entry Site (IRES) that relies on a specific RP for activation. The unique combination of an inhibitor of general translation and an activator of specialized translation is key to ribosome-mediated control of gene expression. Here we discuss how these RNA regulatory elements provide a new level of control to protein expression and their implications for gene expression, organismal development and evolution.
Lei, Ted Chih-Wei; Tseng, Fan-Shuo
2017-07-01
This paper addresses the problem of high-computational complexity decoding in traditional Wyner-Ziv video coding (WZVC). The key focus is the migration of two traditionally high-computationally complex encoder algorithms, namely motion estimation and mode decision. In order to reduce the computational burden in this process, the proposed architecture adopts the partial boundary matching algorithm and four flexible types of block mode decision at the decoder. This approach does away with the need for motion estimation and mode decision at the encoder. The experimental results show that the proposed padding block-based WZVC not only decreases decoder complexity to approximately one hundredth that of the state-of-the-art DISCOVER decoding but also outperforms DISCOVER codec by up to 3 to 4 dB.
Study of bifurcation behavior of two-dimensional turbo product code decoders
International Nuclear Information System (INIS)
He Yejun; Lau, Francis C.M.; Tse, Chi K.
2008-01-01
Turbo codes, low-density parity-check (LDPC) codes and turbo product codes (TPCs) are high performance error-correction codes which employ iterative algorithms for decoding. Under different conditions, the behaviors of the decoders are different. While the nonlinear dynamical behaviors of turbo code decoders and LDPC decoders have been reported in the literature, the dynamical behavior of TPC decoders is relatively unexplored. In this paper, we investigate the behavior of the iterative algorithm of a two-dimensional TPC decoder when the input signal-to-noise ratio (SNR) varies. The quantity to be measured is the mean square value of the posterior probabilities of the information bits. Unlike turbo decoders or LDPC decoders, TPC decoders do not produce a clear 'waterfall region'. This is mainly because the TPC decoding algorithm does not converge to 'indecisive' fixed points even at very low SNR values
Architecture for time or transform domain decoding of reed-solomon codes
Shao, Howard M. (Inventor); Truong, Trieu-Kie (Inventor); Hsu, In-Shek (Inventor); Deutsch, Leslie J. (Inventor)
1989-01-01
Two pipeline (255,233) RS decoders, one a time domain decoder and the other a transform domain decoder, use the same first part to develop an errata locator polynomial .tau.(x), and an errata evaluator polynominal A(x). Both the time domain decoder and transform domain decoder have a modified GCD that uses an input multiplexer and an output demultiplexer to reduce the number of GCD cells required. The time domain decoder uses a Chien search and polynomial evaluator on the GCD outputs .tau.(x) and A(x), for the final decoding steps, while the transform domain decoder uses a transform error pattern algorithm operating on .tau.(x) and the initial syndrome computation S(x), followed by an inverse transform algorithm in sequence for the final decoding steps prior to adding the received RS coded message to produce a decoded output message.
Decoding subjective mental states from fMRI activity patterns
International Nuclear Information System (INIS)
Tamaki, Masako; Kamitani, Yukiyasu
2011-01-01
In recent years, functional magnetic resonance imaging (fMRI) decoding has emerged as a powerful tool to read out detailed stimulus features from multi-voxel brain activity patterns. Moreover, the method has been extended to perform a primitive form of 'mind-reading,' by applying a decoder 'objectively' trained using stimulus features to more 'subjective' conditions. In this paper, we first introduce basic procedures for fMRI decoding based on machine learning techniques. Second, we discuss the source of information used for decoding, in particular, the possibility of extracting information from subvoxel neural structures. We next introduce two experimental designs for decoding subjective mental states: the 'objective-to-subjective design' and the 'subjective-to-subjective design.' Then, we illustrate recent studies on the decoding of a variety of mental states, such as, attention, awareness, decision making, memory, and mental imagery. Finally, we discuss the challenges and new directions of fMRI decoding. (author)
Study of bifurcation behavior of two-dimensional turbo product code decoders
Energy Technology Data Exchange (ETDEWEB)
He Yejun [Department of Electronic and Information Engineering, Hong Kong Polytechnic University, Hunghom, Hong Kong (China); Lau, Francis C.M. [Department of Electronic and Information Engineering, Hong Kong Polytechnic University, Hunghom, Hong Kong (China)], E-mail: encmlau@polyu.edu.hk; Tse, Chi K. [Department of Electronic and Information Engineering, Hong Kong Polytechnic University, Hunghom, Hong Kong (China)
2008-04-15
Turbo codes, low-density parity-check (LDPC) codes and turbo product codes (TPCs) are high performance error-correction codes which employ iterative algorithms for decoding. Under different conditions, the behaviors of the decoders are different. While the nonlinear dynamical behaviors of turbo code decoders and LDPC decoders have been reported in the literature, the dynamical behavior of TPC decoders is relatively unexplored. In this paper, we investigate the behavior of the iterative algorithm of a two-dimensional TPC decoder when the input signal-to-noise ratio (SNR) varies. The quantity to be measured is the mean square value of the posterior probabilities of the information bits. Unlike turbo decoders or LDPC decoders, TPC decoders do not produce a clear 'waterfall region'. This is mainly because the TPC decoding algorithm does not converge to 'indecisive' fixed points even at very low SNR values.
Interpolation decoding method with variable parameters for fractal image compression
International Nuclear Information System (INIS)
He Chuanjiang; Li Gaoping; Shen Xiaona
2007-01-01
The interpolation fractal decoding method, which is introduced by [He C, Yang SX, Huang X. Progressive decoding method for fractal image compression. IEE Proc Vis Image Signal Process 2004;3:207-13], involves generating progressively the decoded image by means of an interpolation iterative procedure with a constant parameter. It is well-known that the majority of image details are added at the first steps of iterations in the conventional fractal decoding; hence the constant parameter for the interpolation decoding method must be set as a smaller value in order to achieve a better progressive decoding. However, it needs to take an extremely large number of iterations to converge. It is thus reasonable for some applications to slow down the iterative process at the first stages of decoding and then to accelerate it afterwards (e.g., at some iteration as we need). To achieve the goal, this paper proposed an interpolation decoding scheme with variable (iteration-dependent) parameters and proved the convergence of the decoding process mathematically. Experimental results demonstrate that the proposed scheme has really achieved the above-mentioned goal
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...... decoding algorithm: an extension of classical key equation decoding which gives a probabilistic decoding algorithm up to the Sudan radius. We show how the resulting key equations can be solved by the matrix minimization algorithms from computer algebra, yielding similar asymptotic complexities....
Dynamics of intracellular information decoding.
Kobayashi, Tetsuya J; Kamimura, Atsushi
2011-10-01
A variety of cellular functions are robust even to substantial intrinsic and extrinsic noise in intracellular reactions and the environment that could be strong enough to impair or limit them. In particular, of substantial importance is cellular decision-making in which a cell chooses a fate or behavior on the basis of information conveyed in noisy external signals. For robust decoding, the crucial step is filtering out the noise inevitably added during information transmission. As a minimal and optimal implementation of such an information decoding process, the autocatalytic phosphorylation and autocatalytic dephosphorylation (aPadP) cycle was recently proposed. Here, we analyze the dynamical properties of the aPadP cycle in detail. We describe the dynamical roles of the stationary and short-term responses in determining the efficiency of information decoding and clarify the optimality of the threshold value of the stationary response and its information-theoretical meaning. Furthermore, we investigate the robustness of the aPadP cycle against the receptor inactivation time and intrinsic noise. Finally, we discuss the relationship among information decoding with information-dependent actions, bet-hedging and network modularity.
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.
Dynamics of intracellular information decoding
International Nuclear Information System (INIS)
Kobayashi, Tetsuya J; Kamimura, Atsushi
2011-01-01
A variety of cellular functions are robust even to substantial intrinsic and extrinsic noise in intracellular reactions and the environment that could be strong enough to impair or limit them. In particular, of substantial importance is cellular decision-making in which a cell chooses a fate or behavior on the basis of information conveyed in noisy external signals. For robust decoding, the crucial step is filtering out the noise inevitably added during information transmission. As a minimal and optimal implementation of such an information decoding process, the autocatalytic phosphorylation and autocatalytic dephosphorylation (aPadP) cycle was recently proposed. Here, we analyze the dynamical properties of the aPadP cycle in detail. We describe the dynamical roles of the stationary and short-term responses in determining the efficiency of information decoding and clarify the optimality of the threshold value of the stationary response and its information-theoretical meaning. Furthermore, we investigate the robustness of the aPadP cycle against the receptor inactivation time and intrinsic noise. Finally, we discuss the relationship among information decoding with information-dependent actions, bet-hedging and network modularity
Performance breakdown in optimal stimulus decoding.
Lubomir Kostal; Lansky, Petr; Pilarski, Stevan
2015-06-01
One of the primary goals of neuroscience is to understand how neurons encode and process information about their environment. The problem is often approached indirectly by examining the degree to which the neuronal response reflects the stimulus feature of interest. In this context, the methods of signal estimation and detection theory provide the theoretical limits on the decoding accuracy with which the stimulus can be identified. The Cramér-Rao lower bound on the decoding precision is widely used, since it can be evaluated easily once the mathematical model of the stimulus-response relationship is determined. However, little is known about the behavior of different decoding schemes with respect to the bound if the neuronal population size is limited. We show that under broad conditions the optimal decoding displays a threshold-like shift in performance in dependence on the population size. The onset of the threshold determines a critical range where a small increment in size, signal-to-noise ratio or observation time yields a dramatic gain in the decoding precision. We demonstrate the existence of such threshold regions in early auditory and olfactory information coding. We discuss the origin of the threshold effect and its impact on the design of effective coding approaches in terms of relevant population size.
Generation of Chimeric RNAs by cis-splicing of adjacent genes (cis-SAGe) in mammals.
Zhuo, Jian-Shu; Jing, Xiao-Yan; Du, Xin; Yang, Xiu-Qin
2018-02-20
Chimeric RNA molecules, possessing exons from two or more independent genes, are traditionally believed to be produced by chromosome rearrangement. However, recent studies revealed that cis-splicing of adjacent genes (cis- SAGe) is one of the major mechanisms underlying the formation of chimeric RNAs. cis-SAGe refers to intergenic splicing of directly adjacent genes with the same transcriptional orientation, resulting in read-through transcripts, termed chimeric RNAs, which contain sequences from two or more parental genes. cis-SAGe was first identified in tumor cells, since then its potential in carcinogenesis has attracted extensive attention. More and more scientists are focusing on it. With the development of research, cis-SAGe was found to be ubiquitous in various normal tissues, and might make a crucial contribution to the formation of novel genes in the evolution of genomes. In this review, we summarize the splicing pattern, expression characteristics, possible mechanisms, and significance of cis-SAGe in mammals. This review will be helpful for general understanding of the current status and development tendency of cis-SAGe.
XcisClique: analysis of regulatory bicliques
Directory of Open Access Journals (Sweden)
Grene Ruth
2006-04-01
Full Text Available Abstract Background Modeling of cis-elements or regulatory motifs in promoter (upstream regions of genes is a challenging computational problem. In this work, set of regulatory motifs simultaneously present in the promoters of a set of genes is modeled as a biclique in a suitably defined bipartite graph. A biologically meaningful co-occurrence of multiple cis-elements in a gene promoter is assessed by the combined analysis of genomic and gene expression data. Greater statistical significance is associated with a set of genes that shares a common set of regulatory motifs, while simultaneously exhibiting highly correlated gene expression under given experimental conditions. Methods XcisClique, the system developed in this work, is a comprehensive infrastructure that associates annotated genome and gene expression data, models known cis-elements as regular expressions, identifies maximal bicliques in a bipartite gene-motif graph; and ranks bicliques based on their computed statistical significance. Significance is a function of the probability of occurrence of those motifs in a biclique (a hypergeometric distribution, and on the new sum of absolute values statistic (SAV that uses Spearman correlations of gene expression vectors. SAV is a statistic well-suited for this purpose as described in the discussion. Results XcisClique identifies new motif and gene combinations that might indicate as yet unidentified involvement of sets of genes in biological functions and processes. It currently supports Arabidopsis thaliana and can be adapted to other organisms, assuming the existence of annotated genomic sequences, suitable gene expression data, and identified regulatory motifs. A subset of Xcis Clique functionalities, including the motif visualization component MotifSee, source code, and supplementary material are available at https://bioinformatics.cs.vt.edu/xcisclique/.
Real-time SHVC software decoding with multi-threaded parallel processing
Gudumasu, Srinivas; He, Yuwen; Ye, Yan; He, Yong; Ryu, Eun-Seok; Dong, Jie; Xiu, Xiaoyu
2014-09-01
This paper proposes a parallel decoding framework for scalable HEVC (SHVC). Various optimization technologies are implemented on the basis of SHVC reference software SHM-2.0 to achieve real-time decoding speed for the two layer spatial scalability configuration. SHVC decoder complexity is analyzed with profiling information. The decoding process at each layer and the up-sampling process are designed in parallel and scheduled by a high level application task manager. Within each layer, multi-threaded decoding is applied to accelerate the layer decoding speed. Entropy decoding, reconstruction, and in-loop processing are pipeline designed with multiple threads based on groups of coding tree units (CTU). A group of CTUs is treated as a processing unit in each pipeline stage to achieve a better trade-off between parallelism and synchronization. Motion compensation, inverse quantization, and inverse transform modules are further optimized with SSE4 SIMD instructions. Simulations on a desktop with an Intel i7 processor 2600 running at 3.4 GHz show that the parallel SHVC software decoder is able to decode 1080p spatial 2x at up to 60 fps (frames per second) and 1080p spatial 1.5x at up to 50 fps for those bitstreams generated with SHVC common test conditions in the JCT-VC standardization group. The decoding performance at various bitrates with different optimization technologies and different numbers of threads are compared in terms of decoding speed and resource usage, including processor and memory.
High-throughput GPU-based LDPC decoding
Chang, Yang-Lang; Chang, Cheng-Chun; Huang, Min-Yu; Huang, Bormin
2010-08-01
Low-density parity-check (LDPC) code is a linear block code known to approach the Shannon limit via the iterative sum-product algorithm. LDPC codes have been adopted in most current communication systems such as DVB-S2, WiMAX, WI-FI and 10GBASE-T. LDPC for the needs of reliable and flexible communication links for a wide variety of communication standards and configurations have inspired the demand for high-performance and flexibility computing. Accordingly, finding a fast and reconfigurable developing platform for designing the high-throughput LDPC decoder has become important especially for rapidly changing communication standards and configurations. In this paper, a new graphic-processing-unit (GPU) LDPC decoding platform with the asynchronous data transfer is proposed to realize this practical implementation. Experimental results showed that the proposed GPU-based decoder achieved 271x speedup compared to its CPU-based counterpart. It can serve as a high-throughput LDPC decoder.
Neuroprosthetic Decoder Training as Imitation Learning.
Merel, Josh; Carlson, David; Paninski, Liam; Cunningham, John P
2016-05-01
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.
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.
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.
On Lattice Sequential Decoding for The Unconstrained AWGN Channel
Abediseid, Walid; Alouini, Mohamed-Slim
2013-01-01
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
Performance-complexity tradeoff in sequential decoding for the unconstrained AWGN channel
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.
Gordon, Kacy L.; Arthur, Robert K.; Ruvinsky, Ilya
2015-01-01
Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements. PMID:26020930
Directory of Open Access Journals (Sweden)
Kacy L Gordon
2015-05-01
Full Text Available Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the functions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25, mec-3 and elt-2 from distantly-related nematode species. These species, Caenorhabditis elegans, its congeneric C. briggsae, and three parasitic species Meloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nematoda. Despite the great phylogenetic distances sampled and the extensive sequence divergence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in sequence they are not conserved in orientation or position. Functional tests reveal that some of these motifs contribute to proper expression. Our results suggest that conserved regulatory circuitry can persist despite considerable turnover within cis elements.
Sun, Hong; Guns, Tias; Fierro, Ana Carolina; Thorrez, Lieven; Nijssen, Siegfried; Marchal, Kathleen
2012-01-01
Computationally retrieving biologically relevant cis-regulatory modules (CRMs) is not straightforward. Because of the large number of candidates and the imperfection of the screening methods, many spurious CRMs are detected that are as high scoring as the biologically true ones. Using ChIP-information allows not only to reduce the regions in which the binding sites of the assayed transcription factor (TF) should be located, but also allows restricting the valid CRMs to those that contain the assayed TF (here referred to as applying CRM detection in a query-based mode). In this study, we show that exploiting ChIP-information in a query-based way makes in silico CRM detection a much more feasible endeavor. To be able to handle the large datasets, the query-based setting and other specificities proper to CRM detection on ChIP-Seq based data, we developed a novel powerful CRM detection method ‘CPModule’. By applying it on a well-studied ChIP-Seq data set involved in self-renewal of mouse embryonic stem cells, we demonstrate how our tool can recover combinatorial regulation of five known TFs that are key in the self-renewal of mouse embryonic stem cells. Additionally, we make a number of new predictions on combinatorial regulation of these five key TFs with other TFs documented in TRANSFAC. PMID:22422841
Trellises and Trellis-Based Decoding Algorithms for Linear Block Codes
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
Singer product apertures—A coded aperture system with a fast decoding algorithm
International Nuclear Information System (INIS)
Byard, Kevin; Shutler, Paul M.E.
2017-01-01
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.
Singer product apertures—A coded aperture system with a fast decoding algorithm
Energy Technology Data Exchange (ETDEWEB)
Byard, Kevin, E-mail: kevin.byard@aut.ac.nz [School of Economics, Faculty of Business, Economics and Law, Auckland University of Technology, Auckland 1142 (New Zealand); Shutler, Paul M.E. [National Institute of Education, Nanyang Technological University, 1 Nanyang Walk, Singapore 637616 (Singapore)
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.
Fast decoding algorithms for coded aperture systems
International Nuclear Information System (INIS)
Byard, Kevin
2014-01-01
Fast decoding algorithms are described for a number of established coded aperture systems. The fast decoding algorithms for all these systems offer significant reductions in the number of calculations required when reconstructing images formed by a coded aperture system and hence require less computation time to produce the images. The algorithms may therefore be of use in applications that require fast image reconstruction, such as near real-time nuclear medicine and location of hazardous radioactive spillage. Experimental tests confirm the efficacy of the fast decoding techniques
LDPC-based iterative joint source-channel decoding for JPEG2000.
Pu, Lingling; Wu, Zhenyu; Bilgin, Ali; Marcellin, Michael W; Vasic, Bane
2007-02-01
A framework is proposed for iterative joint source-channel decoding of JPEG2000 codestreams. At the encoder, JPEG2000 is used to perform source coding with certain error-resilience (ER) modes, and LDPC codes are used to perform channel coding. During decoding, the source decoder uses the ER modes to identify corrupt sections of the codestream and provides this information to the channel decoder. Decoding is carried out jointly in an iterative fashion. Experimental results indicate that the proposed method requires fewer iterations and improves overall system performance.
Deep Learning Methods for Improved Decoding of Linear Codes
Nachmani, Eliya; Marciano, Elad; Lugosch, Loren; Gross, Warren J.; Burshtein, David; Be'ery, Yair
2018-02-01
The problem of low complexity, close to optimal, channel decoding of linear codes with short to moderate block length is considered. It is shown that deep learning methods can be used to improve a standard belief propagation decoder, despite the large example space. Similar improvements are obtained for the min-sum algorithm. It is also shown that tying the parameters of the decoders across iterations, so as to form a recurrent neural network architecture, can be implemented with comparable results. The advantage is that significantly less parameters are required. We also introduce a recurrent neural decoder architecture based on the method of successive relaxation. Improvements over standard belief propagation are also observed on sparser Tanner graph representations of the codes. Furthermore, we demonstrate that the neural belief propagation decoder can be used to improve the performance, or alternatively reduce the computational complexity, of a close to optimal decoder of short BCH codes.
Bayesian population decoding of spiking neurons.
Gerwinn, Sebastian; Macke, Jakob; Bethge, Matthias
2009-01-01
The timing of action potentials in spiking neurons depends on the temporal dynamics of their inputs and contains information about temporal fluctuations in the stimulus. Leaky integrate-and-fire neurons constitute a popular class of encoding models, in which spike times depend directly on the temporal structure of the inputs. However, optimal decoding rules for these models have only been studied explicitly in the noiseless case. Here, we study decoding rules for probabilistic inference of a continuous stimulus from the spike times of a population of leaky integrate-and-fire neurons with threshold noise. We derive three algorithms for approximating the posterior distribution over stimuli as a function of the observed spike trains. In addition to a reconstruction of the stimulus we thus obtain an estimate of the uncertainty as well. Furthermore, we derive a 'spike-by-spike' online decoding scheme that recursively updates the posterior with the arrival of each new spike. We use these decoding rules to reconstruct time-varying stimuli represented by a Gaussian process from spike trains of single neurons as well as neural populations.
Bayesian population decoding of spiking neurons
Directory of Open Access Journals (Sweden)
Sebastian Gerwinn
2009-10-01
Full Text Available The timing of action potentials in spiking neurons depends on the temporal dynamics of their inputs and contains information about temporal fluctuations in the stimulus. Leaky integrate-and-fire neurons constitute a popular class of encoding models, in which spike times depend directly on the temporal structure of the inputs. However, optimal decoding rules for these models have only been studied explicitly in the noiseless case. Here, we study decoding rules for probabilistic inference of a continuous stimulus from the spike times of a population of leaky integrate-and-fire neurons with threshold noise. We derive three algorithms for approximating the posterior distribution over stimuli as a function of the observed spike trains. In addition to a reconstruction of the stimulus we thus obtain an estimate of the uncertainty as well. Furthermore, we derive a `spike-by-spike' online decoding scheme that recursively updates the posterior with the arrival of each new spike. We use these decoding rules to reconstruct time-varying stimuli represented by a Gaussian process from spike trains of single neurons as well as neural populations.
Three phase full wave dc motor decoder
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.
Transcription regulatory networks analysis using CAGE
Tegnér, Jesper N.
2009-10-01
Mapping out cellular networks in general and transcriptional networks in particular has proved to be a bottle-neck hampering our understanding of biological processes. Integrative approaches fusing computational and experimental technologies for decoding transcriptional networks at a high level of resolution is therefore of uttermost importance. Yet, this is challenging since the control of gene expression in eukaryotes is a complex multi-level process influenced by several epigenetic factors and the fine interplay between regulatory proteins and the promoter structure governing the combinatorial regulation of gene expression. In this chapter we review how the CAGE data can be integrated with other measurements such as expression, physical interactions and computational prediction of regulatory motifs, which together can provide a genome-wide picture of eukaryotic transcriptional regulatory networks at a new level of resolution. © 2010 by Pan Stanford Publishing Pte. Ltd. All rights reserved.
Decoding and Encoding Facial Expressions in Preschool-Age Children.
Zuckerman, Miron; Przewuzman, Sylvia J.
1979-01-01
Preschool-age children drew, decoded, and encoded facial expressions depicting five different emotions. Accuracy of drawing, decoding and encoding each of the five emotions was consistent across the three tasks; decoding ability was correlated with drawing ability among female subjects, but neither of these abilities was correlated with encoding…
Belief propagation decoding of quantum channels by passing quantum messages
International Nuclear Information System (INIS)
Renes, Joseph M
2017-01-01
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. (fast track communication)
Belief propagation decoding of quantum channels by passing quantum messages
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.
Directory of Open Access Journals (Sweden)
Lu Tingting
2012-12-01
Full Text Available Abstract Background Cis-natural antisense transcripts (cis-NATs are RNAs transcribed from the antisense strand of a gene locus, and are complementary to the RNA transcribed from the sense strand. Common techniques including microarray approach and analysis of transcriptome databases are the major ways to globally identify cis-NATs in various eukaryotic organisms. Genome-wide in silico analysis has identified a large number of cis-NATs that may generate endogenous short interfering RNAs (nat-siRNAs, which participate in important biogenesis mechanisms for transcriptional and post-transcriptional regulation in rice. However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs. Results We applied high-throughput strand-specific complementary DNA sequencing technology (ssRNA-seq to deeply sequence mRNA for assessing sense and antisense transcripts that were derived under salt, drought and cold stresses, and normal conditions, in the model plant rice (Oryza sativa. Combined with RAP-DB genome annotation (the Rice Annotation Project Database build-5 data set, 76,013 transcripts corresponding to 45,844 unique gene loci were assembled, in which 4873 gene loci were newly identified. Of 3819 putative rice cis-NATs, 2292 were detected as expressed and giving rise to small RNAs from their overlapping regions through integrated analysis of ssRNA-seq data and small RNA data. Among them, 503 cis-NATs seemed to be associated with specific conditions. The deep sequence data from isolated epidermal cells of rice seedlings further showed that 54.0% of cis-NATs were expressed simultaneously in a population of homogenous cells. Nearly 9.7% of rice transcripts were involved in one-to-one or many-to-many cis-NATs formation. Furthermore, only 17.4-34.7% of 223 many-to-many cis-NAT groups were all expressed and generated nat-siRNAs, indicating that only some cis-NAT groups may be involved in complex regulatory networks. Conclusions
International Nuclear Information System (INIS)
Reue, K.; Leff, T.; Breslow, J.L.
1988-01-01
Apolipoprotein CIII (apoCIII) is a major protein constituent of triglyceride-rich lipoproteins and is synthesized primarily in the liver. Cis-acting DNA elements required for liver-specific apoCIII gene transcription were identified with transient expression assays in the human hepatoma (HepG2) and epithelial carcinoma (HeLa) cell lines. In liver cells, 821 nucleotides of the human apoCIII gene 5'-flanking sequence were required for maximum levels of gene expression, while the proximal 110 nucleotides alone were sufficient. No expression was observed in similar studies with HeLa cells. The level of expression was modulated by a combination of positive and negative cis-acting sequences, which interact with distinct sets of proteins from liver and HeLa cell nuclear extracts. The proximal positive regulatory region shares homology with similarly located sequences of other genes strongly expressed in the liver, including α 1 -antitrypsin and other apolipoprotein genes. The negative regulatory region is striking homologous to the human β-interferon gene regulatory element. The distal positive region shares homology with some viral enhancers and has properties of a tissue-specific enhancer. The regulation of the apoCIII gene is complex but shares features with other genes, suggesting shuffling of regulatory elements as a common mechanism for cell type-specific gene expression
Directory of Open Access Journals (Sweden)
Bin Zhang
2012-07-01
Full Text Available Genome-wide studies have identified thousands of long noncoding RNAs (lncRNAs lacking protein-coding capacity. However, most lncRNAs are expressed at a very low level, and in most cases there is no genetic evidence to support their in vivo function. Malat1 (metastasis associated lung adenocarcinoma transcript 1 is among the most abundant and highly conserved lncRNAs, and it exhibits an uncommon 3′-end processing mechanism. In addition, its specific nuclear localization, developmental regulation, and dysregulation in cancer are suggestive of it having a critical biological function. We have characterized a Malat1 loss-of-function genetic model that indicates that Malat1 is not essential for mouse pre- and postnatal development. Furthermore, depletion of Malat1 does not affect global gene expression, splicing factor level and phosphorylation status, or alternative pre-mRNA splicing. However, among a small number of genes that were dysregulated in adult Malat1 knockout mice, many were Malat1 neighboring genes, thus indicating a potential cis-regulatory role of Malat1 gene transcription.
International Nuclear Information System (INIS)
Hoeschele, J.D.; Ferren, L.A.; Roberts, J.A.; Whitfield, L.R.
1983-01-01
The discovery and successful clinical application of the potent anti-tumor compound, cis-Dichlorodiammineplatinum(II), cis-DDP* has stimulated considerable interest in developing effective but less toxic second-generation platinum antitumor drugs. One such candidate drug is cis-Dichloro-trans-dihydroxo-bis-(isopropylamine)platinum(IV), cis-trans-[PtCl 2 (OH) 2 (i-PrNH 2 ) 2 ], (CHIP). An important feature of this Pt(IV) agent is that in addition to exhibiting a generally milder clinical toxicity than cisplatin, the dose-limiting toxicity of CHIP is the more common myelosuppression rather than the less desirable nephrotoxicity. Also, CHIP has been reported recently to be more effective than cisplatin against both alkylating agent sensitive and resistant strains of the Yoshida sarcoms. A microscale synthesis for /sup 195m/Pt-labelled CHIP and the tissue distribution and pharmacokinetic properties of this agent in normal female Fischer 344 rats are reported. A comparison with similar data for /sup 195m/Pt-cis-DDP is included
Decoding Algorithms for Random Linear Network Codes
DEFF Research Database (Denmark)
Heide, Janus; Pedersen, Morten Videbæk; Fitzek, Frank
2011-01-01
We consider the problem of efficient decoding of a random linear code over a finite field. In particular we are interested in the case where the code is random, relatively sparse, and use the binary finite field as an example. The goal is to decode the data using fewer operations to potentially...... 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...
Ionizing radiation sources management in the Commonwealth of Independent States - CIS
International Nuclear Information System (INIS)
Iskra, A.; Bufetova, M.
2006-01-01
Ionizing radiation sources cover a broad band of power: from powerful NPP reactors and research reactors to portable radioisotope ionizing radiation sources applied in medicine, agriculture, industry and in the energy supply systems of remote facilities. At present, scales and use field of radionuclide sources in the CIS have the tendency to increase. In this connection, the issues of ionizing radiation sources management safety at all stages of their life cycle, from production to treatment, have been of a great importance. The materials on ionizing radiation sources inventory and treatment in the CIS (Russia, Armenia, Belarus, Georgia, Kazakhstan, Kyrgyzstan, Tajikistan and Ukraine) are presented in the report. It is shown that in some republics, there is difficulty in ionizing radiation sources accounting and control system; the national regulatory and legal framework bases regulating activity on radioactive sources use, localization and treatment require update. Many problems are connected with the sources beyond state accounting. The problem of ionizing radiation sources use safety is complicated by the growing activity of various terrorist groups. The opportunity to use ionizing radiation sources with terrorism goals requires the application of defined systems of security and physical protection at all stages of their management. For this purpose a collective, with all CIS countries, organization of radioactive sources accounting and control as well as countermeasures on their illegal transportation and use are necessary. In this connection, the information collection regarding situation with providing of ionizing radiation sources safety, conditions of equipment and storage facilities, radioactive materials accounting and control system in the CIS countries is vitally needed
Oppositional Decoding as an Act of Resistance.
Steiner, Linda
1988-01-01
Argues that contributors to the "No Comment" feature of "Ms." magazine are engaging in oppositional decoding and speculates on why this is a satisfying group process. Also notes such decoding presents another challenge to the idea that mass media has the same effect on all audiences. (SD)
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.
Directory of Open Access Journals (Sweden)
Yamaguchi-Shinozaki Kazuko
2011-02-01
Full Text Available Abstract Background Phytohormones organize plant development and environmental adaptation through cell-to-cell signal transduction, and their action involves transcriptional activation. Recent international efforts to establish and maintain public databases of Arabidopsis microarray data have enabled the utilization of this data in the analysis of various phytohormone responses, providing genome-wide identification of promoters targeted by phytohormones. Results We utilized such microarray data for prediction of cis-regulatory elements with an octamer-based approach. Our test prediction of a drought-responsive RD29A promoter with the aid of microarray data for response to drought, ABA and overexpression of DREB1A, a key regulator of cold and drought response, provided reasonable results that fit with the experimentally identified regulatory elements. With this succession, we expanded the prediction to various phytohormone responses, including those for abscisic acid, auxin, cytokinin, ethylene, brassinosteroid, jasmonic acid, and salicylic acid, as well as for hydrogen peroxide, drought and DREB1A overexpression. Totally 622 promoters that are activated by phytohormones were subjected to the prediction. In addition, we have assigned putative functions to 53 octamers of the Regulatory Element Group (REG that have been extracted as position-dependent cis-regulatory elements with the aid of their feature of preferential appearance in the promoter region. Conclusions Our prediction of Arabidopsis cis-regulatory elements for phytohormone responses provides guidance for experimental analysis of promoters to reveal the basis of the transcriptional network of phytohormone responses.
Pla, M; Vilardell, J; Guiltinan, M J; Marcotte, W R; Niogret, M F; Quatrano, R S; Pagès, M
1993-01-01
The maize gene rab28 has been identified as ABA-inducible in embryos and vegetative tissues. It is also induced by water stress in young leaves. The proximal promoter region contains the conserved cis-acting element CCACGTGG (ABRE) reported for ABA induction in other plant genes. Transient expression assays in rice protoplasts indicate that a 134 bp fragment (-194 to -60 containing the ABRE) fused to a truncated cauliflower mosaic virus promoter (35S) is sufficient to confer ABA-responsiveness upon the GUS reporter gene. Gel retardation experiments indicate that nuclear proteins from tissues in which the rab28 gene is expressed can interact specifically with this 134 bp DNA fragment. Nuclear protein extracts from embryo and water-stressed leaves generate specific complexes of different electrophoretic mobility which are stable in the presence of detergent and high salt. However, by DMS footprinting the same guanine-specific contacts with the ABRE in both the embryo and leaf binding activities were detected. These results indicate that the rab28 promoter sequence CCACGTGG is a functional ABA-responsive element, and suggest that distinct regulatory factors with apparent similar affinity for the ABRE sequence may be involved in the hormone action during embryo development and in vegetative tissues subjected to osmotic stress.
Jin, Yuanxiang; Wang, Jiangcong; Sun, Xueqing; Ye, Yang; Xu, Minjie; Wang, Jianai; Chen, Shaoping; Fu, Zhengwei
2013-12-01
The commercial bifenthrin (BF) contains two cis isomers. In the present study, a dose of 15mg/kg of 1R-cis-BF or 1S-cis-BF was orally administered for 3 weeks to female mice before or during pregnancy. Then, the expression of steroidogenesis related genes which were considered as effective biomarkers of endocrine disruption were analyzed in the male offspring. Maternal exposure to 1S-cis-BF during pregnancy significantly reduced the mRNA levels of peripheral benzodiazepine receptor (PBR) and steroidogenic acute regulatory protein (StAR) in the testes of 3- or 6-week old male offspring. In addition, a significant decrease of cytochrome P450 17α-hydroxysteroid dehydrogenase (P450-17α) was also observed in the testes of 6-week old male offspring when dams were treated with 1S-cis-BF during pregnancy but not before pregnancy. Moreover, the scavenger receptor class B type 1 (SRB1) and cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc) decreased significantly in the testes of 6-week old male offspring when dams were treated with 1S-cis-BF during and before pregnancy. Thus, oral administration of the maternal mice to cis-BF for 3 weeks, particularly during pregnancy, resulted in endocrine disruption in the male offspring, with the 1S-cis-BF causing more significant alterations than the 1R-cis-BF form. Copyright © 2013 Elsevier Inc. All rights reserved.
Detection of Weakly Conserved Ancestral Mammalian RegulatorySequences by Primate Comparisons
Energy Technology Data Exchange (ETDEWEB)
Wang, Qian-fei; Prabhakar, Shyam; Chanan, Sumita; Cheng,Jan-Fang; Rubin, Edward M.; Boffelli, Dario
2006-06-01
Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detectcryptic functional elements, which are too weakly conserved among mammalsto distinguish from nonfunctional DNA. To address this problem, weexplored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved in cholesterol homeostasis, in 6 nonhumanprimates. Our analysis identified 6 noncoding DNA elements displayingsignificant conservation among primates, but undetectable in more distantcomparisons. In vitro and in vivo tests revealed that at least three ofthese 6 elements have regulatory function. Notably, the mouse orthologsof these three functional human sequences had regulatory activity despitetheir lack of significant sequence conservation, indicating that they arecryptic ancestral cis-regulatory elements. These regulatory elementscould still be detected in a smaller set of three primate speciesincluding human, rhesus and marmoset. Since the human and rhesus genomesequences are already available, and the marmoset genome is activelybeing sequenced, the primate-specific conservation analysis describedhere can be applied in the near future on a whole-genome scale, tocomplement the annotation provided by more distant speciescomparisons.
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....
Ueno, Tetsuro; Yasumasu, Shigeki; Hayashi, Shinji; Iuchi, Ichiro
2004-07-01
Choriogenins (chg-H, chg-L) are precursor proteins of egg envelope of medaka and synthesized in the spawning female liver in response to estrogen. We linked a gene construct chg-L1.5 kb/GFP (a 1.5 kb 5'-upstream region of the chg-L gene fused with a green fluorescence protein (GFP) gene) to another construct emgb/RFP (a cis-regulatory region of embryonic globin gene fused with an RFP gene), injected the double fusion gene construct into 1- or 2-cell-stage embryos, and selected embryos expressing the RFP in erythroid cells. From the embryos, we established two lines of chg-L1.5 kb/GFP-emgb/RFP-transgenic medaka. The 3-month-old spawning females and estradiol-17beta (E2)-exposed males displayed the liver-specific GFP expression. The E2-dependent GFP expression was detected in the differentiating liver of the stage 37-38 embryos. In addition, RT-PCR and whole-mount in situ hybridization showed that the E2-dependent chg expression was found in the liver of the stage 34 embryos of wild medaka, suggesting that such E2-dependency is achieved shortly after differentiation of the liver. Analysis using serial deletion mutants fused with GFP showed that the region -426 to -284 of the chg-L gene or the region -364 to -265 of the chg-H gene had the ability to promote the E2-dependent liver-specific GFP expression of its downstream gene. Further analyses suggested that an estrogen response element (ERE) at -309, an ERE half-site at -330 and a binding site for C/EBP at -363 of the chg-L gene played important roles in its downstream chg-L gene expression. In addition, this transgenic medaka may be useful as one of the test animals for detecting environmental estrogenic steroids.
Locally decodable codes and private information retrieval schemes
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
Turbo decoder architecture for beyond-4G applications
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
Mapping visual stimuli to perceptual decisions via sparse decoding of mesoscopic neural activity.
Sajda, Paul
2010-01-01
In this talk I will describe our work investigating sparse decoding of neural activity, given a realistic mapping of the visual scene to neuronal spike trains generated by a model of primary visual cortex (V1). We use a linear decoder which imposes sparsity via an L1 norm. The decoder can be viewed as a decoding neuron (linear summation followed by a sigmoidal nonlinearity) in which there are relatively few non-zero synaptic weights. We find: (1) the best decoding performance is for a representation that is sparse in both space and time, (2) decoding of a temporal code results in better performance than a rate code and is also a better fit to the psychophysical data, (3) the number of neurons required for decoding increases monotonically as signal-to-noise in the stimulus decreases, with as little as 1% of the neurons required for decoding at the highest signal-to-noise levels, and (4) sparse decoding results in a more accurate decoding of the stimulus and is a better fit to psychophysical performance than a distributed decoding, for example one imposed by an L2 norm. We conclude that sparse coding is well-justified from a decoding perspective in that it results in a minimum number of neurons and maximum accuracy when sparse representations can be decoded from the neural dynamics.
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,…
Decoding using back-project algorithm from coded image in ICF
International Nuclear Information System (INIS)
Jiang shaoen; Liu Zhongli; Zheng Zhijian; Tang Daoyuan
1999-01-01
The principle of the coded imaging and its decoding in inertial confinement fusion is described simply. The authors take ring aperture microscope for example and use back-project (BP) algorithm to decode the coded image. The decoding program has been performed for numerical simulation. Simulations of two models are made, and the results show that the accuracy of BP algorithm is high and effect of reconstruction is good. Thus, it indicates that BP algorithm is applicable to decoding for coded image in ICF experiments
2012-04-20
...: The financial markets as a whole should benefit from [limit order display] because the price discovery... revised tier sizes and corresponding liquidity minimum amounts are in the best interest of the market for...-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing of Amendment No. 1...
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.
Efficient universal computing architectures for decoding neural activity.
Directory of Open Access Journals (Sweden)
Benjamin I Rapoport
Full Text Available The ability to decode neural activity into meaningful control signals for prosthetic devices is critical to the development of clinically useful brain- machine interfaces (BMIs. Such systems require input from tens to hundreds of brain-implanted recording electrodes in order to deliver robust and accurate performance; in serving that primary function they should also minimize power dissipation in order to avoid damaging neural tissue; and they should transmit data wirelessly in order to minimize the risk of infection associated with chronic, transcutaneous implants. Electronic architectures for brain- machine interfaces must therefore minimize size and power consumption, while maximizing the ability to compress data to be transmitted over limited-bandwidth wireless channels. Here we present a system of extremely low computational complexity, designed for real-time decoding of neural signals, and suited for highly scalable implantable systems. Our programmable architecture is an explicit implementation of a universal computing machine emulating the dynamics of a network of integrate-and-fire neurons; it requires no arithmetic operations except for counting, and decodes neural signals using only computationally inexpensive logic operations. The simplicity of this architecture does not compromise its ability to compress raw neural data by factors greater than [Formula: see text]. We describe a set of decoding algorithms based on this computational architecture, one designed to operate within an implanted system, minimizing its power consumption and data transmission bandwidth; and a complementary set of algorithms for learning, programming the decoder, and postprocessing the decoded output, designed to operate in an external, nonimplanted unit. The implementation of the implantable portion is estimated to require fewer than 5000 operations per second. A proof-of-concept, 32-channel field-programmable gate array (FPGA implementation of this portion
Robust pattern decoding in shape-coded structured light
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.
Coding and decoding with dendrites.
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.
Optimal and efficient decoding of concatenated quantum block codes
International Nuclear Information System (INIS)
Poulin, David
2006-01-01
We consider the problem of optimally decoding a quantum error correction code--that is, to find the optimal recovery procedure given the outcomes of partial ''check'' measurements on the system. In general, this problem is NP hard. However, we demonstrate that for concatenated block codes, the optimal decoding can be efficiently computed using a message-passing algorithm. We compare the performance of the message-passing algorithm to that of the widespread blockwise hard decoding technique. Our Monte Carlo results using the five-qubit and Steane's code on a depolarizing channel demonstrate significant advantages of the message-passing algorithms in two respects: (i) Optimal decoding increases by as much as 94% the error threshold below which the error correction procedure can be used to reliably send information over a noisy channel; and (ii) for noise levels below these thresholds, the probability of error after optimal decoding is suppressed at a significantly higher rate, leading to a substantial reduction of the error correction overhead
Error Recovery Properties and Soft Decoding of Quasi-Arithmetic Codes
Directory of Open Access Journals (Sweden)
Christine Guillemot
2007-08-01
Full Text Available This paper first introduces a new set of aggregated state models for soft-input decoding of quasi arithmetic (QA codes with a termination constraint. The decoding complexity with these models is linear with the sequence length. The aggregation parameter controls the tradeoff between decoding performance and complexity. It is shown that close-to-optimal decoding performance can be obtained with low values of the aggregation parameter, that is, with a complexity which is significantly reduced with respect to optimal QA bit/symbol models. The choice of the aggregation parameter depends on the synchronization recovery properties of the QA codes. This paper thus describes a method to estimate the probability mass function (PMF of the gain/loss of symbols following a single bit error (i.e., of the difference between the number of encoded and decoded symbols. The entropy of the gain/loss turns out to be the average amount of information conveyed by a length constraint on both the optimal and aggregated state models. This quantity allows us to choose the value of the aggregation parameter that will lead to close-to-optimal decoding performance. It is shown that the optimum position for the length constraint is not the last time instant of the decoding process. This observation leads to the introduction of a new technique for robust decoding of QA codes with redundancy which turns out to outperform techniques based on the concept of forbidden symbol.
Word Processing in Dyslexics: An Automatic Decoding Deficit?
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)
On the decoding process in ternary error-correcting output codes.
Escalera, Sergio; Pujol, Oriol; Radeva, Petia
2010-01-01
A common way to model multiclass classification problems is to design a set of binary classifiers and to combine them. Error-Correcting Output Codes (ECOC) represent a successful framework to deal with these type of problems. Recent works in the ECOC framework showed significant performance improvements by means of new problem-dependent designs based on the ternary ECOC framework. The ternary framework contains a larger set of binary problems because of the use of a "do not care" symbol that allows us to ignore some classes by a given classifier. However, there are no proper studies that analyze the effect of the new symbol at the decoding step. In this paper, we present a taxonomy that embeds all binary and ternary ECOC decoding strategies into four groups. We show that the zero symbol introduces two kinds of biases that require redefinition of the decoding design. A new type of decoding measure is proposed, and two novel decoding strategies are defined. We evaluate the state-of-the-art coding and decoding strategies over a set of UCI Machine Learning Repository data sets and into a real traffic sign categorization problem. The experimental results show that, following the new decoding strategies, the performance of the ECOC design is significantly improved.
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.
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.
LDPC Codes--Structural Analysis and Decoding Techniques
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,…
Tong, Pin; Monahan, Jack; Prendergast, James G D
2017-03-01
Large-scale gene expression datasets are providing an increasing understanding of the location of cis-eQTLs in the human genome and their role in disease. However, little is currently known regarding the extent of regulatory site-sharing between genes. This is despite it having potentially wide-ranging implications, from the determination of the way in which genetic variants may shape multiple phenotypes to the understanding of the evolution of human gene order. By first identifying the location of non-redundant cis-eQTLs, we show that regulatory site-sharing is a relatively common phenomenon in the human genome, with over 10% of non-redundant regulatory variants linked to the expression of multiple nearby genes. We show that these shared, local regulatory sites are linked to high levels of chromatin looping between the regulatory sites and their associated genes. In addition, these co-regulated gene modules are found to be strongly conserved across mammalian species, suggesting that shared regulatory sites have played an important role in shaping human gene order. The association of these shared cis-eQTLs with multiple genes means they also appear to be unusually important in understanding the genetics of human phenotypes and pleiotropy, with shared regulatory sites more often linked to multiple human phenotypes than other regulatory variants. This study shows that regulatory site-sharing is likely an underappreciated aspect of gene regulation and has important implications for the understanding of various biological phenomena, including how the two and three dimensional structures of the genome have been shaped and the potential causes of disease pleiotropy outside coding regions.
A novel method for predicting activity of cis-regulatory modules, based on a diverse training set.
Yang, Wei; Sinha, Saurabh
2017-01-01
With the rapid emergence of technologies for locating cis-regulatory modules (CRMs) genome-wide, the next pressing challenge is to assign precise functions to each CRM, i.e. to determine the spatiotemporal domains or cell-types where it drives expression. A popular approach to this task is to model the typical k-mer composition of a set of CRMs known to drive a common expression pattern, and assign that pattern to other CRMs exhibiting a similar k-mer composition. This approach does not rely on prior knowledge of transcription factors relevant to the CRM or their binding motifs, and is thus more widely applicable than motif-based methods for predicting CRM activity, but is also prone to false positive predictions. We present a novel strategy to improve the above-mentioned approach: to predict if a CRM drives a specific gene expression pattern, assess not only how similar the CRM is to other CRMs with similar activity but also to CRMs with distinct activities. We use a state-of-the-art statistical method to quantify a CRM's sequence similarity to many different training sets of CRMs, and employ a classification algorithm to integrate these similarity scores into a single prediction of the CRM's activity. This strategy is shown to significantly improve CRM activity prediction over current approaches. Our implementation of the new method, called IMMBoost, is freely available as source code, at https://github.com/weiyangedward/IMMBoost CONTACT: sinhas@illinois.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Takahashi, T; Guron, C; Shetty, S; Matsui, H; Raghow, R
1997-09-05
To dissect the cis-regulatory elements of the murine Msx-1 promoter, which lacks a conventional TATA element, a putative Msx-1 promoter DNA fragment (from -1282 to +106 base pairs (bp)) or its congeners containing site-specific alterations were fused to luciferase reporter and introduced into NIH3T3 and C2C12 cells, and the expression of luciferase was assessed in transient expression assays. The functional consequences of the sequential 5' deletions of the promotor revealed that multiple positive and negative regulatory elements participate in regulating transcription of the Msx-1 gene. Surprisingly, however, the optimal expression of Msx-1 promoter in either NIH3T3 or C2C12 cells required only 165 bp of the upstream sequence to warrant detailed examination of its structure. Therefore, the functional consequences of site-specific deletions and point mutations of the cis-acting elements of the minimal Msx-1 promoter were systematically examined. Concomitantly, potential transcriptional factor(s) interacting with the cis-acting elements of the minimal promoter were also studied by gel electrophoretic mobility shift assays and DNase I footprinting. Combined analyses of the minimal promoter by DNase I footprinting, electrophoretic mobility shift assays, and super shift assays with specific antibodies revealed that 5'-flanking regions from -161 to -154 and from -26 to -13 of the Msx-1 promoter contains an authentic E box (proximal E box), capable of binding a protein immunologically related to the upstream stimulating factor 1 (USF-1) and a GC-rich sequence motif which can bind to Sp1 (proximal Sp1), respectively. Additionally, we observed that the promoter activation was seriously hampered if the proximal E box was removed or mutated, and the promoter activity was eliminated completely if the proximal Sp1 site was similarly altered. Absolute dependence of the Msx-1 minimal promoter on Sp1 could be demonstrated by transient expression assays in the Sp1-deficient
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....
Design of FBG En/decoders in Coherent 2-D Time-polarization OCDMA Systems
Hou, Fen-fei; Yang, Ming
2012-12-01
A novel fiber Bragg grating (FBG)-based en/decoder for the two-dimensional (2-D) time-spreading and polarization multiplexer optical coding is proposed. Compared with other 2-D en/decoders, the proposed en/decoding for an optical code-division multiple-access (OCDMA) system uses a single phase-encoded FBG and coherent en/decoding. Furthermore, combined with reconstruction-equivalent-chirp technology, such en/decoders can be realized with a conventional simple fabrication setup. Experimental results of such en/decoders and the corresponding system test at a data rate of 5 Gbit/s demonstrate that this kind of 2-D FBG-based en/decoders could improve the performances of OCDMA systems.
Low Complexity List Decoding for Polar Codes with Multiple CRC Codes
Directory of Open Access Journals (Sweden)
Jong-Hwan Kim
2017-04-01
Full Text Available Polar codes are the first family of error correcting codes that provably achieve the capacity of symmetric binary-input discrete memoryless channels with low complexity. Since the development of polar codes, there have been many studies to improve their finite-length performance. As a result, polar codes are now adopted as a channel code for the control channel of 5G new radio of the 3rd generation partnership project. However, the decoder implementation is one of the big practical problems and low complexity decoding has been studied. This paper addresses a low complexity successive cancellation list decoding for polar codes utilizing multiple cyclic redundancy check (CRC codes. While some research uses multiple CRC codes to reduce memory and time complexity, we consider the operational complexity of decoding, and reduce it by optimizing CRC positions in combination with a modified decoding operation. Resultingly, the proposed scheme obtains not only complexity reduction from early stopping of decoding, but also additional reduction from the reduced number of decoding paths.
Yang, Fan; Wang, Jiebiao; Pierce, Brandon L; Chen, Lin S
2017-11-01
The impact of inherited genetic variation on gene expression in humans is well-established. The majority of known expression quantitative trait loci (eQTLs) impact expression of local genes ( cis -eQTLs). More research is needed to identify effects of genetic variation on distant genes ( trans -eQTLs) and understand their biological mechanisms. One common trans -eQTLs mechanism is "mediation" by a local ( cis ) transcript. Thus, mediation analysis can be applied to genome-wide SNP and expression data in order to identify transcripts that are " cis -mediators" of trans -eQTLs, including those " cis -hubs" involved in regulation of many trans -genes. Identifying such mediators helps us understand regulatory networks and suggests biological mechanisms underlying trans -eQTLs, both of which are relevant for understanding susceptibility to complex diseases. The multitissue expression data from the Genotype-Tissue Expression (GTEx) program provides a unique opportunity to study cis -mediation across human tissue types. However, the presence of complex hidden confounding effects in biological systems can make mediation analyses challenging and prone to confounding bias, particularly when conducted among diverse samples. To address this problem, we propose a new method: Genomic Mediation analysis with Adaptive Confounding adjustment (GMAC). It enables the search of a very large pool of variables, and adaptively selects potential confounding variables for each mediation test. Analyses of simulated data and GTEx data demonstrate that the adaptive selection of confounders by GMAC improves the power and precision of mediation analysis. Application of GMAC to GTEx data provides new insights into the observed patterns of cis -hubs and trans -eQTL regulation across tissue types. © 2017 Yang et al.; Published by Cold Spring Harbor Laboratory Press.
Decoding bipedal locomotion from the rat sensorimotor cortex
Rigosa, J.; Panarese, A.; Dominici, N.; Friedli, L.; van den Brand, R.; Carpaneto, J.; DiGiovanna, J.; Courtine, G.; Micera, S.
2015-01-01
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
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.
Performance-complexity tradeoff in sequential decoding for the unconstrained AWGN channel
Abediseid, Walid; Alouini, Mohamed-Slim
2013-01-01
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
Neural network decoder for quantum error correcting codes
Krastanov, Stefan; Jiang, Liang
Artificial neural networks form a family of extremely powerful - albeit still poorly understood - tools used in anything from image and sound recognition through text generation to, in our case, decoding. We present a straightforward Recurrent Neural Network architecture capable of deducing the correcting procedure for a quantum error-correcting code from a set of repeated stabilizer measurements. We discuss the fault-tolerance of our scheme and the cost of training the neural network for a system of a realistic size. Such decoders are especially interesting when applied to codes, like the quantum LDPC codes, that lack known efficient decoding schemes.
Distributed coding/decoding complexity in video sensor networks.
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.
Best linear decoding of random mask images
International Nuclear Information System (INIS)
Woods, J.W.; Ekstrom, M.P.; Palmieri, T.M.; Twogood, R.E.
1975-01-01
In 1968 Dicke proposed coded imaging of x and γ rays via random pinholes. Since then, many authors have agreed with him that this technique can offer significant image improvement. A best linear decoding of the coded image is presented, and its superiority over the conventional matched filter decoding is shown. Experimental results in the visible light region are presented. (U.S.)
Observations on Polar Coding with CRC-Aided List Decoding
2016-09-01
TECHNICAL REPORT 3041 September 2016 Observations on Polar Coding with CRC-Aided List Decoding David Wasserman Approved for public release. SSC...described in [2, 3]. In FY15 and FY16 we used cyclic redundancy check (CRC)-aided polar list decoding [4]. Section 2 describes the basics of polar coding ...and gives details of the encoders and decoders we used. In the course of our research, we performed simulations of polar codes in hundreds of cases
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....
cis sequence effects on gene expression
Directory of Open Access Journals (Sweden)
Jacobs Kevin
2007-08-01
Full Text Available Abstract Background Sequence and transcriptional variability within and between individuals are typically studied independently. The joint analysis of sequence and gene expression variation (genetical genomics provides insight into the role of linked sequence variation in the regulation of gene expression. We investigated the role of sequence variation in cis on gene expression (cis sequence effects in a group of genes commonly studied in cancer research in lymphoblastoid cell lines. We estimated the proportion of genes exhibiting cis sequence effects and the proportion of gene expression variation explained by cis sequence effects using three different analytical approaches, and compared our results to the literature. Results We generated gene expression profiling data at N = 697 candidate genes from N = 30 lymphoblastoid cell lines for this study and used available candidate gene resequencing data at N = 552 candidate genes to identify N = 30 candidate genes with sufficient variance in both datasets for the investigation of cis sequence effects. We used two additive models and the haplotype phylogeny scanning approach of Templeton (Tree Scanning to evaluate association between individual SNPs, all SNPs at a gene, and diplotypes, with log-transformed gene expression. SNPs and diplotypes at eight candidate genes exhibited statistically significant (p cis sequence effects in our study, respectively. Conclusion Based on analysis of our results and the extant literature, one in four genes exhibits significant cis sequence effects, and for these genes, about 30% of gene expression variation is accounted for by cis sequence variation. Despite diverse experimental approaches, the presence or absence of significant cis sequence effects is largely supported by previously published studies.
Emotion Decoding and Incidental Processing Fluency as Antecedents of Attitude Certainty.
Petrocelli, John V; Whitmire, Melanie B
2017-07-01
Previous research demonstrates that attitude certainty influences the degree to which an attitude changes in response to persuasive appeals. In the current research, decoding emotions from facial expressions and incidental processing fluency, during attitude formation, are examined as antecedents of both attitude certainty and attitude change. In Experiment 1, participants who decoded anger or happiness during attitude formation expressed their greater attitude certainty, and showed more resistance to persuasion than participants who decoded sadness. By manipulating the emotion decoded, the diagnosticity of processing fluency experienced during emotion decoding, and the gaze direction of the social targets, Experiment 2 suggests that the link between emotion decoding and attitude certainty results from incidental processing fluency. Experiment 3 demonstrated that fluency in processing irrelevant stimuli influences attitude certainty, which in turn influences resistance to persuasion. Implications for appraisal-based accounts of attitude formation and attitude change are discussed.
Lu, Kun Ping; Kondo, Asami; Albayram, Onder; Herbert, Megan K; Liu, Hekun; Zhou, Xiao Zhen
2016-11-01
Alzheimer disease (AD) and chronic traumatic encephalopathy (CTE) share a common neuropathologic signature-neurofibrillary tangles made of phosphorylated tau-but do not have the same pathogenesis or symptoms. Although whether traumatic brain injury (TBI) could cause AD has not been established, CTE is shown to be associated with TBI. Until recently, whether and how TBI leads to tau-mediated neurodegeneration was unknown. The unique prolyl isomerase Pin1 protects against the development of tau-mediated neurodegeneration in AD by converting the phosphorylated Thr231-Pro motif in tau (ptau) from the pathogenic cis conformation to the physiologic trans conformation, thereby restoring ptau function. The recent development of antibodies able to distinguish and eliminate both conformations specifically has led to the discovery of cis-ptau as a precursor of tau-induced pathologic change and an early driver of neurodegeneration that directly links TBI to CTE and possibly to AD. Within hours of TBI in mice or neuronal stress in vitro, neurons prominently produce cis-ptau, which causes and spreads cis-ptau pathologic changes, termed cistauosis. Cistauosis eventually leads to widespread tau-mediated neurodegeneration and brain atrophy. Cistauosis is effectively blocked by the cis-ptau antibody, which targets intracellular cis-ptau for proteasome-mediated degradation and prevents extracellular cis-ptau from spreading to other neurons. Treating TBI mice with cis-ptau antibody not only blocks early cistauosis but also prevents development and spreading of tau-mediated neurodegeneration and brain atrophy and restores brain histopathologic features and functional outcomes. Thus, cistauosis is a common early disease mechanism for AD, TBI, and CTE, and cis-ptau and its antibody may be useful for early diagnosis, treatment, and prevention of these devastating diseases.
On Lattice Sequential Decoding for Large MIMO Systems
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
Finding cis-regulatory modules in Drosophila using phylogenetic hidden Markov models
DEFF Research Database (Denmark)
Wong, Wendy S W; Nielsen, Rasmus
2007-01-01
MOTIVATION: Finding the regulatory modules for transcription factors binding is an important step in elucidating the complex molecular mechanisms underlying regulation of gene expression. There are numerous methods available for solving this problem, however, very few of them take advantage of th...
Sequential decoders for large MIMO systems
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.
Adaptive decoding of MPEG-4 sprites for memory-constrained embedded systems
Pastrnak, M.; Farin, D.S.; With, de P.H.N.; Cardinal, J.; Cerf, N.; Delgrnage, O.
2005-01-01
Background sprite decoding is an essential part of object-based video coding.The composition and rendering of a final scene involves the placing of individual video objects in a predefined way superimposed on the decoded background image. The MPEG-4 standard includes the decoding algorithm for
Low Power LDPC Code Decoder Architecture Based on Intermediate Message Compression Technique
Shimizu, Kazunori; Togawa, Nozomu; Ikenaga, Takeshi; Goto, Satoshi
Reducing the power dissipation for LDPC code decoder is a major challenging task to apply it to the practical digital communication systems. In this paper, we propose a low power LDPC code decoder architecture based on an intermediate message-compression technique which features as follows: (i) An intermediate message compression technique enables the decoder to reduce the required memory capacity and write power dissipation. (ii) A clock gated shift register based intermediate message memory architecture enables the decoder to decompress the compressed messages in a single clock cycle while reducing the read power dissipation. The combination of the above two techniques enables the decoder to reduce the power dissipation while keeping the decoding throughput. The simulation results show that the proposed architecture improves the power efficiency up to 52% and 18% compared to that of the decoder based on the overlapped schedule and the rapid convergence schedule without the proposed techniques respectively.
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...
Multiformat decoder for a DSP-based IP set-top box
Pescador, F.; Garrido, M. J.; Sanz, C.; Juárez, E.; Samper, D.; Antoniello, R.
2007-05-01
Internet Protocol Set-Top Boxes (IP STBs) based on single-processor architectures have been recently introduced in the market. In this paper, the implementation of an MPEG-4 SP/ASP video decoder for a multi-format IP STB based on a TMS320DM641 DSP is presented. An initial decoder for PC platform was fully tested and ported to the DSP. Using this code an optimization process was started achieving a 90% speedup. This process allows real-time MPEG-4 SP/ASP decoding. The MPEG-4 decoder has been integrated in an IP STB and tested in a real environment using DVD movies and TV channels with excellent results.
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.
Visual perception as retrospective Bayesian decoding from high- to low-level features.
Ding, Stephanie; Cueva, Christopher J; Tsodyks, Misha; Qian, Ning
2017-10-24
When a stimulus is presented, its encoding is known to progress from low- to high-level features. How these features are decoded to produce perception is less clear, and most models assume that decoding follows the same low- to high-level hierarchy of encoding. There are also theories arguing for global precedence, reversed hierarchy, or bidirectional processing, but they are descriptive without quantitative comparison with human perception. Moreover, observers often inspect different parts of a scene sequentially to form overall perception, suggesting that perceptual decoding requires working memory, yet few models consider how working-memory properties may affect decoding hierarchy. We probed decoding hierarchy by comparing absolute judgments of single orientations and relative/ordinal judgments between two sequentially presented orientations. We found that lower-level, absolute judgments failed to account for higher-level, relative/ordinal judgments. However, when ordinal judgment was used to retrospectively decode memory representations of absolute orientations, striking aspects of absolute judgments, including the correlation and forward/backward aftereffects between two reported orientations in a trial, were explained. We propose that the brain prioritizes decoding of higher-level features because they are more behaviorally relevant, and more invariant and categorical, and thus easier to specify and maintain in noisy working memory, and that more reliable higher-level decoding constrains less reliable lower-level decoding. Published under the PNAS license.
An Improved Unscented Kalman Filter Based Decoder for Cortical Brain-Machine Interfaces.
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.
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 decoders....
Locating and decoding barcodes in fuzzy images captured by smart phones
Deng, Wupeng; Hu, Jiwei; Liu, Quan; Lou, Ping
2017-07-01
With the development of barcodes for commercial use, people's requirements for detecting barcodes by smart phone become increasingly pressing. The low quality of barcode image captured by mobile phone always affects the decoding and recognition rates. This paper focuses on locating and decoding EAN-13 barcodes in fuzzy images. We present a more accurate locating algorithm based on segment length and high fault-tolerant rate algorithm for decoding barcodes. Unlike existing approaches, location algorithm is based on the edge segment length of EAN -13 barcodes, while our decoding algorithm allows the appearance of fuzzy region in barcode image. Experimental results are performed on damaged, contaminated and scratched digital images, and provide a quite promising result for EAN -13 barcode location and decoding.
Merrill, Raymond G.; Goodliff, Kandyce E.; Mazanek, Daniel D.; Reeves, John D., Jr.
2012-01-01
Historically, when mounting expeditions into uncharted territories, explorers have established strategically positioned base camps to pre-position required equipment and consumables. These base camps are secure, safe positions from which expeditions can depart when conditions are favorable, at which technology and operations can be tested and validated, and facilitate timely access to more robust facilities in the event of an emergency. For human exploration missions into deep space, cis-lunar space is well suited to serve as such a base camp. The outer regions of cis-lunar space, such as the Earth-Moon Lagrange points, lie near the edge of Earth s gravity well, allowing equipment and consumables to be aggregated with easy access to deep space and to the lunar surface, as well as more distant destinations, such as near-Earth Asteroids (NEAs) and Mars and its moons. Several approaches to utilizing a cis-lunar base camp for sustainable human exploration, as well as some possible future applications are identified. The primary objective of the analysis presented in this paper is to identify options, show the macro trends, and provide information that can be used as a basis for more detailed mission development. Compared within are the high-level performance and cost of 15 preliminary cis-lunar exploration campaigns that establish the capability to conduct crewed missions of up to one year in duration, and then aggregate mass in cis-lunar space to facilitate an expedition from Cis-Lunar Base Camp. Launch vehicles, chemical propulsion stages, and electric propulsion stages are discussed and parametric sizing values are used to create architectures of in-space transportation elements that extend the existing in-space supply chain to cis-lunar space. The transportation options to cis-lunar space assessed vary in efficiency by almost 50%; from 0.16 to 0.68 kg of cargo in cis-lunar space for every kilogram of mass in Low Earth Orbit (LEO). For the 15 cases, 5-year campaign
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 reduct......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...
Decoding algorithm for vortex communications receiver
Kupferman, Judy; Arnon, Shlomi
2018-01-01
Vortex light beams can provide a tremendous alphabet for encoding information. We derive a symbol decoding algorithm for a direct detection matrix detector vortex beam receiver using Laguerre Gauss (LG) modes, and develop a mathematical model of symbol error rate (SER) for this receiver. We compare SER as a function of signal to noise ratio (SNR) for our algorithm and for the Pearson correlation algorithm. To our knowledge, this is the first comprehensive treatment of a decoding algorithm of a matrix detector for an LG receiver.
Behnam, Babak; Iuchi, Satoshi; Fujita, Miki; Fujita, Yasunari; Takasaki, Hironori; Osakabe, Yuriko; Yamaguchi-Shinozaki, Kazuko; Kobayashi, Masatomo; Shinozaki, Kazuo
2013-01-01
Plants respond to dehydration stress and tolerate water-deficit status through complex physiological and cellular processes. Many genes are induced by water deficit. Abscisic acid (ABA) plays important roles in tolerance to dehydration stress by inducing many stress genes. ABA is synthesized de novo in response to dehydration. Most of the genes involved in ABA biosynthesis have been identified, and they are expressed mainly in leaf vascular tissues. Of the products of such genes, 9-cis-epoxycarotenoid dioxygenase (NCED) is a key enzyme in ABA biosynthesis. One of the five NCED genes in Arabidopsis, AtNCED3, is significantly induced by dehydration. To understand the regulatory mechanism of the early stages of the dehydration stress response, it is important to analyse the transcriptional regulatory systems of AtNCED3. In the present study, we found that an overlapping G-box recognition sequence (5′-CACGTG-3′) at −2248 bp from the transcriptional start site of AtNCED3 is an important cis-acting element in the induction of the dehydration response. We discuss the possible transcriptional regulatory system of dehydration-responsive AtNCED3 expression, and how this may control the level of ABA under water-deficit conditions. PMID:23604098
Fast and Flexible Successive-Cancellation List Decoders for Polar Codes
Hashemi, Seyyed Ali; Condo, Carlo; Gross, Warren J.
2017-11-01
Polar codes have gained significant amount of attention during the past few years and have been selected as a coding scheme for the next generation of mobile broadband standard. Among decoding schemes, successive-cancellation list (SCL) decoding provides a reasonable trade-off between the error-correction performance and hardware implementation complexity when used to decode polar codes, at the cost of limited throughput. The simplified SCL (SSCL) and its extension SSCL-SPC increase the speed of decoding by removing redundant calculations when encountering particular information and frozen bit patterns (rate one and single parity check codes), while keeping the error-correction performance unaltered. In this paper, we improve SSCL and SSCL-SPC by proving that the list size imposes a specific number of bit estimations required to decode rate one and single parity check codes. Thus, the number of estimations can be limited while guaranteeing exactly the same error-correction performance as if all bits of the code were estimated. We call the new decoding algorithms Fast-SSCL and Fast-SSCL-SPC. Moreover, we show that the number of bit estimations in a practical application can be tuned to achieve desirable speed, while keeping the error-correction performance almost unchanged. Hardware architectures implementing both algorithms are then described and implemented: it is shown that our design can achieve 1.86 Gb/s throughput, higher than the best state-of-the-art decoders.
Hard decoding algorithm for optimizing thresholds under general Markovian noise
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.
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.
Firing rate estimation using infinite mixture models and its application to neural decoding.
Shibue, Ryohei; Komaki, Fumiyasu
2017-11-01
Neural decoding is a framework for reconstructing external stimuli from spike trains recorded by various neural recordings. Kloosterman et al. proposed a new decoding method using marked point processes (Kloosterman F, Layton SP, Chen Z, Wilson MA. J Neurophysiol 111: 217-227, 2014). This method does not require spike sorting and thereby improves decoding accuracy dramatically. In this method, they used kernel density estimation to estimate intensity functions of marked point processes. However, the use of kernel density estimation causes problems such as low decoding accuracy and high computational costs. To overcome these problems, we propose a new decoding method using infinite mixture models to estimate intensity. The proposed method improves decoding performance in terms of accuracy and computational speed. We apply the proposed method to simulation and experimental data to verify its performance. NEW & NOTEWORTHY We propose a new neural decoding method using infinite mixture models and nonparametric Bayesian statistics. The proposed method improves decoding performance in terms of accuracy and computation speed. We have successfully applied the proposed method to position decoding from spike trains recorded in a rat hippocampus. Copyright © 2017 the American Physiological Society.
Cis-trans photoisomerization of abscisic acid
International Nuclear Information System (INIS)
Brabham, D.E.; Biggs, R.H.
1981-01-01
An important regulator of numerous physiological processes in higher plants is abscisic acid (ABA), which is photoisomerized from the more biologically active cis isomer to the nearly inactive trans isomer by natural sunlight. It is possible that this photoisomerization is a UV control mechanism in functions regulated by ABA. The quantum yields of both the cis to trans and trans to cis photoisomerizations were measured under various conditions of pH and oxygen concentration at room temperature. The yield for photoisomerization of cis-ABA ranged from 0.25 at pH 3.0 to 0.11 at pH 7.0. Oxygen partially quenched the process. The quantum yield varied only slightly with wavelength. The quantum yield of photolysis of cis-ABA was reported for pH 3.0 as 0.06. This yield also varied slightly with wavelength and was relatively insensitive to oxygen. This relatively high yield explains the loss of potency of ABA during UV irradiation. Phosphorescence of cis- and trans-ABA was observed in methanol at 77 K. Onset of the emission was at 350 nm. The emission spectra were the same for both isomers. From these results a mechanism of UV action on plants based on the photoisomerization of the inactive trans-ABA to the biologically active cis isomer is proposed. (author)
High-speed architecture for the decoding of trellis-coded modulation
Osborne, William P.
1992-01-01
Since 1971, when the Viterbi Algorithm was introduced as the optimal method of decoding convolutional codes, improvements in circuit technology, especially VLSI, have steadily increased its speed and practicality. Trellis-Coded Modulation (TCM) combines convolutional coding with higher level modulation (non-binary source alphabet) to provide forward error correction and spectral efficiency. For binary codes, the current stare-of-the-art is a 64-state Viterbi decoder on a single CMOS chip, operating at a data rate of 25 Mbps. Recently, there has been an interest in increasing the speed of the Viterbi Algorithm by improving the decoder architecture, or by reducing the algorithm itself. Designs employing new architectural techniques are now in existence, however these techniques are currently applied to simpler binary codes, not to TCM. The purpose of this report is to discuss TCM architectural considerations in general, and to present the design, at the logic gate level, or a specific TCM decoder which applies these considerations to achieve high-speed decoding.
RNA regulatory elements and polyadenylation in plants
Directory of Open Access Journals (Sweden)
Arthur G. Hunt
2012-01-01
Full Text Available Alternative poly(A site choice (also known as alternative polyadenylation, or APA has the potential to affect gene expression in qualitative and quantitative ways. Alternative polyadenylation may affect as many as 82% of all expressed genes in a plant. The consequences of APA include the generation of transcripts with differing 3’-UTRs (and thus differing potential regulatory potential and of transcripts with differing protein-coding potential. Genome-wide studies of possible APA suggest a linkage with pre-mRNA splicing, and indicate a coincidence of and perhaps cooperation between RNA regulatory elements that affect splicing efficiency and the recognition of novel intronic poly(A sites. These studies also raise the possibility of the existence of a novel class of polyadenylation-related cis elements that are distinct from the well-characterized plant polyadenylation signal. Many potential APA events, however, have not been associated with identifiable cis elements. The present state of the field reveals a broad scope of APA, and also numerous opportunities for research into mechanisms that govern both choice and regulation of poly(A sites in plants.
Piecing together cis-regulatory networks: insights from epigenomics studies in plants.
Huang, Shao-Shan C; Ecker, Joseph R
2018-05-01
5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell. Methylome and transcriptome dynamics have been investigated in development and environmental responses in Arabidopsis and agriculturally and ecologically important plants, revealing the interdependent relationship among genomic context, methylation patterns, and expression of TE and protein coding genes. Analyses of methylome variation among plant natural populations and species have begun to quantify the extent of genetic control of methylome variation vs. true epimutation, and model the evolutionary forces driving methylome evolution in both short and long time scales. The ability of DNA methylation to positively or negatively modulate binding affinity of transcription factors (TFs) provides a natural link from genome sequence and methylation changes to transcription. Technologies that allow systematic determination of methylation sensitivities of TFs, in native genomic and methylation context without confounding factors such as histone modifications, will provide baseline datasets for building cell-type- and individual-specific regulatory networks that underlie the establishment and inheritance of complex traits. This article is categorized under: Laboratory Methods and Technologies > Genetic/Genomic Methods Biological Mechanisms > Regulatory Biology. © 2017 Wiley
Armstrong, David R; Garden, Jennifer A; Kennedy, Alan R; Leenhouts, Sarah M; Mulvey, Robert E; O'Keefe, Philip; O'Hara, Charles T; Steven, Alan
2013-01-01
Most recent advances in metallation chemistry have centred on the bulky secondary amide 2,2,6,6-tetramethylpiperidide (TMP) within mixed metal, often ate, compositions. However, the precursor amine TMP(H) is rather expensive so a cheaper substitute would be welcome. Thus this study was aimed towards developing cheaper non-TMP based mixed-metal bases and, as cis-2,6-dimethylpiperidide (cis-DMP) was chosen as the alternative amide, developing cis-DMP zincate chemistry which has received meagre attention compared to that of its methyl-rich counterpart TMP. A new lithium diethylzincate, [(TMEDA)LiZn(cis-DMP)Et2] (TMEDA=N,N,N′,N′-tetramethylethylenediamine) has been synthesised by co-complexation of Li(cis-DMP), Et2Zn and TMEDA, and characterised by NMR (including DOSY) spectroscopy and X-ray crystallography, which revealed a dinuclear contact ion pair arrangement. By using N,N-diisopropylbenzamide as a test aromatic substrate, the deprotonative reactivity of [(TMEDA)LiZn(cis-DMP)Et2] has been probed and contrasted with that of the known but previously uninvestigated di-tert-butylzincate, [(TMEDA)LiZn(cis-DMP)tBu2]. The former was found to be the superior base (for example, producing the ortho-deuteriated product in respective yields of 78 % and 48 % following D2O quenching of zincated benzamide intermediates). An 88 % yield of 2-iodo-N,N-diisopropylbenzamide was obtained on reaction of two equivalents of the diethylzincate with the benzamide followed by iodination. Comparisons are also drawn using 1,1,1,3,3,3-hexamethyldisilazide (HMDS), diisopropylamide and TMP as the amide component in the lithium amide, Et2Zn and TMEDA system. Under certain conditions, the cis-DMP base system was found to give improved results in comparison to HMDS and diisopropylamide (DA), and comparable results to a TMP system. Two novel complexes isolated from reactions of the di-tert-butylzincate and crystallographically characterised, namely the pre-metallation complex [{(iPr)2N(Ph)C=O}LiZn(cis
Electrophysiological difference between mental state decoding and mental state reasoning.
Cao, Bihua; Li, Yiyuan; Li, Fuhong; Li, Hong
2012-06-29
Previous studies have explored the neural mechanism of Theory of Mind (ToM), but the neural correlates of its two components, mental state decoding and mental state reasoning, remain unclear. In the present study, participants were presented with various photographs, showing an actor looking at 1 of 2 objects, either with a happy or an unhappy expression. They were asked to either decode the emotion of the actor (mental state decoding task), predict which object would be chosen by the actor (mental state reasoning task), or judge at which object the actor was gazing (physical task), while scalp potentials were recorded. Results showed that (1) the reasoning task elicited an earlier N2 peak than the decoding task did over the prefrontal scalp sites; and (2) during the late positive component (240-440 ms), the reasoning task elicited a more positive deflection than the other two tasks did at the prefrontal scalp sites. In addition, neither the decoding task nor the reasoning task has no left/right hemisphere difference. These findings imply that mental state reasoning differs from mental state decoding early (210 ms) after stimulus onset, and that the prefrontal lobe is the neural basis of mental state reasoning. Copyright © 2012 Elsevier B.V. All rights reserved.
Partially blind instantly decodable network codes for lossy feedback environment
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.
de Moraes, M de L; Polakiewicz, B; Mattua, M F; Tavares, M F
1998-01-01
Atracurium besylate is a highly selective nondepolarizing neuromuscular blocking agent routinely used during anesthetic procedures. The commercial presentation of this drug is a mixture of positional isomers, cis-cis, cis-trans, and trans-trans. Reversed-phase high-performance liquid chromatography has been the technique of choice for the analysis of atracurium besylate formulations at the quality control laboratory of Núcleo de Desenvolvimento Cristália (São Paulo, Brazil), a local pharmaceutical company. HPLC analysis is usually conducted under gradient elution using acetonitrile/0.1 M phosphate buffer eluent mixture as mobile phase and an octadecyl silica (ODS)-packed column. The complete elution of the three isomers takes about 1 hr. In this work, an alternative capillary electrophoresis methodology was developed. The complete resolution of all three isomers was accomplished in about 13 min (+20 kV/72 cm, 211 nm direct detection) using a 60-mM phosphate buffer solution (pH 4) containing 20 mM beta-cyclodextrin and 4 M urea. The isomer ratio was found to be 59.1% cis-cis, 35.9% cis-trans, and 5.02% trans-trans (expected ratio: 59:35:6). Laudanosine, a major metabolite of atracurium besylate, was identified in two commercially available formulations, Tracur (Núcleo de Desenvolvimento Cristália) and Tracrium (Glaxo Wellcome, S.A., Rio de Janeiro, Brazil). Its concentration increases considerably during storage of the product, even if the product is stored at low temperatures.
Complexity Analysis of Reed-Solomon Decoding over GF without Using Syndromes
Directory of Open Access Journals (Sweden)
Chen Ning
2008-01-01
Full Text Available Abstract There has been renewed interest in decoding Reed-Solomon (RS codes without using syndromes recently. In this paper, we investigate the complexity of syndromeless decoding, and compare it to that of syndrome-based decoding. Aiming to provide guidelines to practical applications, our complexity analysis focuses on RS codes over characteristic-2 fields, for which some multiplicative FFT techniques are not applicable. Due to moderate block lengths of RS codes in practice, our analysis is complete, without big notation. In addition to fast implementation using additive FFT techniques, we also consider direct implementation, which is still relevant for RS codes with moderate lengths. For high-rate RS codes, when compared to syndrome-based decoding algorithms, not only syndromeless decoding algorithms require more field operations regardless of implementation, but also decoder architectures based on their direct implementations have higher hardware costs and lower throughput. We also derive tighter bounds on the complexities of fast polynomial multiplications based on Cantor's approach and the fast extended Euclidean algorithm.
A quantum algorithm for Viterbi decoding of classical convolutional codes
Grice, Jon R.; Meyer, David A.
2014-01-01
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 $Q$ and short decode frames $N$. Other applications of the classical Viterbi algorithm where $Q$ 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 butter...
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.
Multiuser Random Coding Techniques for Mismatched Decoding
Scarlett, Jonathan; Martinez, Alfonso; Guillén i Fàbregas, Albert
2016-01-01
This paper studies multiuser random coding techniques for channel coding with a given (possibly suboptimal) decoding rule. For the mismatched discrete memoryless multiple-access channel, an error exponent is obtained that is tight with respect to the ensemble average, and positive within the interior of Lapidoth's achievable rate region. This exponent proves the ensemble tightness of the exponent of Liu and Hughes in the case of maximum-likelihood decoding. An equivalent dual form of Lapidoth...
Kernel Temporal Differences for Neural Decoding
Bae, Jihye; Sanchez Giraldo, Luis G.; Pohlmeyer, Eric A.; Francis, Joseph T.; Sanchez, Justin C.; Príncipe, José C.
2015-01-01
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. PMID:25866504
Row Reduction Applied to Decoding of Rank Metric and Subspace Codes
DEFF Research Database (Denmark)
Puchinger, Sven; Nielsen, Johan Sebastian Rosenkilde; Li, Wenhui
2017-01-01
We show that decoding of ℓ-Interleaved Gabidulin codes, as well as list-ℓ decoding of Mahdavifar–Vardy (MV) codes can be performed by row reducing skew polynomial matrices. Inspired by row reduction of F[x] matrices, we develop a general and flexible approach of transforming matrices over skew...... polynomial rings into a certain reduced form. We apply this to solve generalised shift register problems over skew polynomial rings which occur in decoding ℓ-Interleaved Gabidulin codes. We obtain an algorithm with complexity O(ℓμ2) where μ measures the size of the input problem and is proportional...... to the code length n in the case of decoding. Further, we show how to perform the interpolation step of list-ℓ-decoding MV codes in complexity O(ℓn2), where n is the number of interpolation constraints....
Coding/decoding two-dimensional images with orbital angular momentum of light.
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.
ESVD: An Integrated Energy Scalable Framework for Low-Power Video Decoding Systems
Directory of Open Access Journals (Sweden)
Wen Ji
2010-01-01
Full Text Available Video applications using mobile wireless devices are a challenging task due to the limited capacity of batteries. The higher complex functionality of video decoding needs high resource requirements. Thus, power efficient control has become more critical design with devices integrating complex video processing techniques. Previous works on power efficient control in video decoding systems often aim at the low complexity design and not explicitly consider the scalable impact of subfunctions in decoding process, and seldom consider the relationship with the features of compressed video date. This paper is dedicated to developing an energy-scalable video decoding (ESVD strategy for energy-limited mobile terminals. First, ESVE can dynamically adapt the variable energy resources due to the device aware technique. Second, ESVD combines the decoder control with decoded data, through classifying the data into different partition profiles according to its characteristics. Third, it introduces utility theoretical analysis during the resource allocation process, so as to maximize the resource utilization. Finally, it adapts the energy resource as different energy budget and generates the scalable video decoding output under energy-limited systems. Experimental results demonstrate the efficiency of the proposed approach.
Cellular automaton decoders of topological quantum memories in the fault tolerant setting
International Nuclear Information System (INIS)
Herold, Michael; Eisert, Jens; Kastoryano, Michael J; Campbell, Earl T
2017-01-01
Active error decoding and correction of topological quantum codes—in particular the toric code—remains one of the most viable routes to large scale quantum information processing. In contrast, passive error correction relies on the natural physical dynamics of a system to protect encoded quantum information. However, the search is ongoing for a completely satisfactory passive scheme applicable to locally interacting two-dimensional systems. Here, we investigate dynamical decoders that provide passive error correction by embedding the decoding process into local dynamics. We propose a specific discrete time cellular-automaton decoder in the fault tolerant setting and provide numerical evidence showing that the logical qubit has a survival time extended by several orders of magnitude over that of a bare unencoded qubit. We stress that (asynchronous) dynamical decoding gives rise to a Markovian dissipative process. We hence equate cellular-automaton decoding to a fully dissipative topological quantum memory, which removes errors continuously. In this sense, uncontrolled and unwanted local noise can be corrected for by a controlled local dissipative process. We analyze the required resources, commenting on additional polylogarithmic factors beyond those incurred by an ideal constant resource dynamical decoder. (paper)
International Nuclear Information System (INIS)
Anon.
1993-01-01
On October 16, 1992, the U.S. Department of Commerce (DOC) settled the antidumping case against the CIS republics by imposing price and volume quotas on CIS uranium imported into the United States. Bound by a suspension agreement, each of the six uranium-producing CIS republics is responsible for restricting the flow of imports to the US-either directly or indirectly. (As the NUKEM Market Report went to press, the Ukraine government notified the DOC of its intent not to terminate the suspension agreement.) This action is to prevent undercutting price levels in the US domestic uranium markets. What follows are ten points about everything you should know about importing uranium from the uranium-producing CIS republics- Kazakhstan, Kyrgyzstan, Russian Federation, Tajikistan, Ukraine and Uzbekistan. Newcomers to the CIS scene should follow this simple roadmap and be aware of the issues they face as importers in terms of Commerce/Customs requirements and documentation and where to get them, when to buy the material and how to transport it, how to deal effectively with CIS exporters, and how to avoid unnecessary complications when buying CIS
Delay reduction in lossy intermittent feedback for generalized instantly decodable network coding
Douik, Ahmed S.
2013-10-01
In this paper, we study the effect of lossy intermittent feedback loss events on the multicast decoding delay performance of generalized instantly decodable network coding. These feedback loss events create uncertainty at the sender about the reception statues of different receivers and thus uncertainty to accurately determine subsequent instantly decodable coded packets. To solve this problem, we first identify the different possibilities of uncertain packets at the sender and their probabilities. We then derive the expression of the mean decoding delay. We formulate the Generalized Instantly Decodable Network Coding (G-IDNC) minimum decoding delay problem as a maximum weight clique problem. Since finding the optimal solution is NP-hard, we design a variant of the algorithm employed in [1]. Our algorithm is compared to the two blind graph update proposed in [2] through extensive simulations. Results show that our algorithm outperforms the blind approaches in all the situations and achieves a tolerable degradation, against the perfect feedback, for large feedback loss period. © 2013 IEEE.
Delay reduction in lossy intermittent feedback for generalized instantly decodable network coding
Douik, Ahmed S.; Sorour, Sameh; Alouini, Mohamed-Slim; Ai-Naffouri, Tareq Y.
2013-01-01
In this paper, we study the effect of lossy intermittent feedback loss events on the multicast decoding delay performance of generalized instantly decodable network coding. These feedback loss events create uncertainty at the sender about the reception statues of different receivers and thus uncertainty to accurately determine subsequent instantly decodable coded packets. To solve this problem, we first identify the different possibilities of uncertain packets at the sender and their probabilities. We then derive the expression of the mean decoding delay. We formulate the Generalized Instantly Decodable Network Coding (G-IDNC) minimum decoding delay problem as a maximum weight clique problem. Since finding the optimal solution is NP-hard, we design a variant of the algorithm employed in [1]. Our algorithm is compared to the two blind graph update proposed in [2] through extensive simulations. Results show that our algorithm outperforms the blind approaches in all the situations and achieves a tolerable degradation, against the perfect feedback, for large feedback loss period. © 2013 IEEE.
Utilizing Cross-Layer Information to Improve Performance in JPEG2000 Decoding
Directory of Open Access Journals (Sweden)
Hannes Persson
2007-01-01
Full Text Available We focus on wireless multimedia communication and investigate how cross-layer information can be used to improve performance at the application layer, using JPEG2000 as an example. The cross-layer information is in the form of soft information from the physical layer. The soft information, which is supplied by a soft decision demodulator, yields reliability measures for the received bits and is fed into two soft input iterative JPEG2000 image decoders. When errors are detected with the error detecting mechanisms in JPEG2000, the decoders utilize the soft information to point out likely transmission errors. Hence, the decoders can correct errors and increase the image quality without making time-consuming retransmissions. We believe that the proposed decoding method utilizing soft information is suitable for a general IP-based network and that it keeps the principles of a layered structure of the protocol stack intact. Further, experimental results with images transmitted over a simulated wireless channel show that a simple decoding algorithm that utilizes soft information can give high gains in image quality compared to the standard hard-decision decoding.
Efficient Dual Domain Decoding of Linear Block Codes Using Genetic Algorithms
Directory of Open Access Journals (Sweden)
Ahmed Azouaoui
2012-01-01
Full Text Available A computationally efficient algorithm for decoding block codes is developed using a genetic algorithm (GA. The proposed algorithm uses the dual code in contrast to the existing genetic decoders in the literature that use the code itself. Hence, this new approach reduces the complexity of decoding the codes of high rates. We simulated our algorithm in various transmission channels. The performance of this algorithm is investigated and compared with competitor decoding algorithms including Maini and Shakeel ones. The results show that the proposed algorithm gives large gains over the Chase-2 decoding algorithm and reach the performance of the OSD-3 for some quadratic residue (QR codes. Further, we define a new crossover operator that exploits the domain specific information and compare it with uniform and two point crossover. The complexity of this algorithm is also discussed and compared to other algorithms.
Optimal coding-decoding for systems controlled via a communication channel
Yi-wei, Feng; Guo, Ge
2013-12-01
In this article, we study the problem of controlling plants over a signal-to-noise ratio (SNR) constrained communication channel. Different from previous research, this article emphasises the importance of the actual channel model and coder/decoder in the study of network performance. Our major objectives include coder/decoder design for an additive white Gaussian noise (AWGN) channel with both standard network configuration and Youla parameter network architecture. We find that the optimal coder and decoder can be realised for different network configuration. The results are useful in determining the minimum channel capacity needed in order to stabilise plants over communication channels. The coder/decoder obtained can be used to analyse the effect of uncertainty on the channel capacity. An illustrative example is provided to show the effectiveness of the results.
Sheikh, Alireza; Amat, Alexandre Graell i.; Liva, Gianluigi
2017-12-01
We analyze the achievable information rates (AIRs) for coded modulation schemes with QAM constellations with both bit-wise and symbol-wise decoders, corresponding to the case where a binary code is used in combination with a higher-order modulation using the bit-interleaved coded modulation (BICM) paradigm and to the case where a nonbinary code over a field matched to the constellation size is used, respectively. In particular, we consider hard decision decoding, which is the preferable option for fiber-optic communication systems where decoding complexity is a concern. Recently, Liga \\emph{et al.} analyzed the AIRs for bit-wise and symbol-wise decoders considering what the authors called \\emph{hard decision decoder} which, however, exploits \\emph{soft information} of the transition probabilities of discrete-input discrete-output channel resulting from the hard detection. As such, the complexity of the decoder is essentially the same as the complexity of a soft decision decoder. In this paper, we analyze instead the AIRs for the standard hard decision decoder, commonly used in practice, where the decoding is based on the Hamming distance metric. We show that if standard hard decision decoding is used, bit-wise decoders yield significantly higher AIRs than symbol-wise decoders. As a result, contrary to the conclusion by Liga \\emph{et al.}, binary decoders together with the BICM paradigm are preferable for spectrally-efficient fiber-optic systems. We also design binary and nonbinary staircase codes and show that, in agreement with the AIRs, binary codes yield better performance.
cis-Bifenthrin enantioselectively induces hepatic oxidative stress in mice.
Jin, Yuanxiang; Wang, Jiangcong; Pan, Xiuhong; Wang, Linggang; Fu, Zhengwei
2013-09-01
Bifenthrin (BF), as a chiral synthetic pyrethroid, is widely used to control field and household pests. In China, the commercial cis-BF contained two enantiomers including 1R-cis-BF and 1S-cis-BF. However, the difference in oxidative stress induced by the two enantiomers in mice still remains unclear. In the present study, 4 week-old adolescent male ICR mice were orally administered cis-BF, 1R-cis-BF or 1S-cis-BF daily for 2, 4 and 6 weeks at doses of 5 mg/kg/day, respectively. We found that the hepatic reactive oxygen species (ROS) levels, as well as the malondialdehyde (MDA) and glutathione (GSH) content both in the serum and liver increased significantly in the 4 or 6 weeks 1S-cis-BF treated groups. The activities of superoxide dismutase (SOD) and catalase (CAT) also changed significantly in the serum and liver of 1S-cis-BF treated mice. More importantly, the significant differences in MDA content and CAT activity both in the serum and liver, and the activities of total antioxidant capacity (T-AOC) and SOD in serum were also observed between the 1S-cis-BF and 1R-cis-BF treated groups. Moreover, the transcription of oxidative stress response related genes including Sod1, Cat and heme oxygenase-1(Ho-1) in the liver of 1S-cis-BF treated groups were also significant higher than those in 1R-cis-BF treated group. Thus, it was concluded that cis-BF induced hepatic oxidative stress in an enantiomer specific manner in mice when exposed during the puberty, and that 1S-cis-BF showed much more toxic in hepatic oxidative stress than 1R-cis-BF. Copyright © 2013 Elsevier Inc. All rights reserved.
CisLunar Habitat Internal Architecture Design Criteria
Jones, R.; Kennedy, K.; Howard, R.; Whitmore, M.; Martin, C.; Garate, J.
2017-01-01
BACKGROUND: In preparation for human exploration to Mars, there is a need to define the development and test program that will validate deep space operations and systems. In that context, a Proving Grounds CisLunar habitat spacecraft is being defined as the next step towards this goal. This spacecraft will operate differently from the ISS or other spacecraft in human history. The performance envelope of this spacecraft (mass, volume, power, specifications, etc.) is being defined by the Future Capabilities Study Team. This team has recognized the need for a human-centered approach for the internal architecture of this spacecraft and has commissioned a CisLunar Phase-1 Habitat Internal Architecture Study Team to develop a NASA reference configuration, providing the Agency with a "smart buyer" approach for future acquisition. THE CISLUNAR HABITAT INTERNAL ARCHITECTURE STUDY: Overall, the CisLunar Habitat Internal Architecture study will address the most significant questions and risks in the current CisLunar architecture, habitation, and operations concept development. This effort is achieved through definition of design criteria, evaluation criteria and process, design of the CisLunar Habitat Phase-1 internal architecture, and the development and fabrication of internal architecture concepts combined with rigorous and methodical Human-in-the-Loop (HITL) evaluations and testing of the conceptual innovations in a controlled test environment. The vision of the CisLunar Habitat Internal Architecture Study is to design, build, and test a CisLunar Phase-1 Habitat Internal Architecture that will be used for habitation (e.g. habitability and human factors) evaluations. The evaluations will mature CisLunar habitat evaluation tools, guidelines, and standards, and will interface with other projects such as the Advanced Exploration Systems (AES) Program integrated Power, Avionics, Software (iPAS), and Logistics for integrated human-in-the-loop testing. The mission of the Cis
Decoding error-correcting codes with Gröbner bases
Bulygin, S.; Pellikaan, G.R.; Veldhuis, R.; Cronie, H.; Hoeksema, H.
2007-01-01
The decoding of arbitrary linear block codes is accomplished by solving a system of quadratic equations by means of Buchberger’s algorithm for finding a Gröbner basis. This generalizes the algorithm of Berlekamp-Massey for decoding Reed Solomon, Goppa and cyclic codes up to half the true minimum
Decoding Individual Finger Movements from One Hand Using Human EEG Signals
Gonzalez, Jania; Ding, Lei
2014-01-01
Brain computer interface (BCI) is an assistive technology, which decodes neurophysiological signals generated by the human brain and translates them into control signals to control external devices, e.g., wheelchairs. One problem challenging noninvasive BCI technologies is the limited control dimensions from decoding movements of, mainly, large body parts, e.g., upper and lower limbs. It has been reported that complicated dexterous functions, i.e., finger movements, can be decoded in electrocorticography (ECoG) signals, while it remains unclear whether noninvasive electroencephalography (EEG) signals also have sufficient information to decode the same type of movements. Phenomena of broadband power increase and low-frequency-band power decrease were observed in EEG in the present study, when EEG power spectra were decomposed by a principal component analysis (PCA). These movement-related spectral structures and their changes caused by finger movements in EEG are consistent with observations in previous ECoG study, as well as the results from ECoG data in the present study. The average decoding accuracy of 77.11% over all subjects was obtained in classifying each pair of fingers from one hand using movement-related spectral changes as features to be decoded using a support vector machine (SVM) classifier. The average decoding accuracy in three epilepsy patients using ECoG data was 91.28% with the similarly obtained features and same classifier. Both decoding accuracies of EEG and ECoG are significantly higher than the empirical guessing level (51.26%) in all subjects (pEEG as in ECoG, and demonstrates the feasibility of discriminating finger movements from one hand using EEG. These findings are promising to facilitate the development of BCIs with rich control signals using noninvasive technologies. PMID:24416360
Gupta, Neha; Parihar, Priyanka; Neema, Vaibhav
2018-04-01
Researchers have proposed many circuit techniques to reduce leakage power dissipation in memory cells. If we want to reduce the overall power in the memory system, we have to work on the input circuitry of memory architecture i.e. row and column decoder. In this research work, low leakage power with a high speed row and column decoder for memory array application is designed and four new techniques are proposed. In this work, the comparison of cluster DECODER, body bias DECODER, source bias DECODER, and source coupling DECODER are designed and analyzed for memory array application. Simulation is performed for the comparative analysis of different DECODER design parameters at 180 nm GPDK technology file using the CADENCE tool. Simulation results show that the proposed source bias DECODER circuit technique decreases the leakage current by 99.92% and static energy by 99.92% at a supply voltage of 1.2 V. The proposed circuit also improves dynamic power dissipation by 5.69%, dynamic PDP/EDP 65.03% and delay 57.25% at 1.2 V supply voltage.
Systolic array processing of the sequential decoding algorithm
Chang, C. Y.; Yao, K.
1989-01-01
A systolic array processing technique is applied to implementing the stack algorithm form of the sequential decoding algorithm. It is shown that sorting, a key function in the stack algorithm, can be efficiently realized by a special type of systolic arrays known as systolic priority queues. Compared to the stack-bucket algorithm, this approach is shown to have the advantages that the decoding always moves along the optimal path, that it has a fast and constant decoding speed and that its simple and regular hardware architecture is suitable for VLSI implementation. Three types of systolic priority queues are discussed: random access scheme, shift register scheme and ripple register scheme. The property of the entries stored in the systolic priority queue is also investigated. The results are applicable to many other basic sorting type problems.
Directory of Open Access Journals (Sweden)
Sean eMaceachern
2012-01-01
Full Text Available Marek’s disease (MD is a commercially important neoplastic disease of chickens caused by Marek’s disease virus (MDV, an oncogenic alphaherpesvirus. Selecting for increased genetic resistance to MD is a control strategy that can augment vaccinal control measures. To identify high-confidence candidate MD resistance genes, we conducted a genome-wide screen for allele-specific expression (ASE amongst F1 progeny of two inbred chicken lines that differ in MD resistance. High throughput sequencing was used to profile transcriptomes from pools of uninfected and infected individuals at 4 days post-infection to identify any genes showing ASE in response to MDV infection. RNA sequencing identified 22,655 single nucleotide polymorphisms (SNPs of which 5,360 in 3,773 genes exhibited significant allelic imbalance. Illumina GoldenGate assays were subsequently used to quantify regulatory variation controlled at the gene (cis and elsewhere in the genome (trans by examining differences in expression between F1 individuals and artificial F1 RNA pools over 6 time periods in 1,536 of the most significant SNPs identified by RNA sequencing. Allelic imbalance as a result of cis-regulatory changes was confirmed in 861 of the 1,233 GoldenGate assays successfully examined. Furthermore we have identified 7 genes that display trans-regulation only in infected animals and approximately 500 SNP that show a complex interaction between cis- and trans-regulatory changes. Our results indicate ASE analyses are a powerful approach to identify regulatory variation responsible for differences in transcript abundance in genes underlying complex traits. And the genes with SNPs exhibiting ASE provide a strong foundation to further investigate the causative polymorphisms and genetic mechanisms for MD resistance. Finally, the methods used here for identifying specific genes and SNPs may have practical implications for applying marker-assisted selection to complex traits that are
Techniques and Architectures for Hazard-Free Semi-Parallel Decoding of LDPC Codes
Directory of Open Access Journals (Sweden)
Rovini Massimo
2009-01-01
Full Text Available The layered decoding algorithm has recently been proposed as an efficient means for the decoding of low-density parity-check (LDPC codes, thanks to the remarkable improvement in the convergence speed (2x of the decoding process. However, pipelined semi-parallel decoders suffer from violations or "hazards" between consecutive updates, which not only violate the layered principle but also enforce the loops in the code, thus spoiling the error correction performance. This paper describes three different techniques to properly reschedule the decoding updates, based on the careful insertion of "idle" cycles, to prevent the hazards of the pipeline mechanism. Also, different semi-parallel architectures of a layered LDPC decoder suitable for use with such techniques are analyzed. Then, taking the LDPC codes for the wireless local area network (IEEE 802.11n as a case study, a detailed analysis of the performance attained with the proposed techniques and architectures is reported, and results of the logic synthesis on a 65 nm low-power CMOS technology are shown.
Online decoding of object-based attention using real-time fMRI.
Niazi, Adnan M; van den Broek, Philip L C; Klanke, Stefan; Barth, Markus; Poel, Mannes; Desain, Peter; van Gerven, Marcel A J
2014-01-01
Visual attention is used to selectively filter relevant information depending on current task demands and goals. Visual attention is called object-based attention when it is directed to coherent forms or objects in the visual field. This study used real-time functional magnetic resonance imaging for moment-to-moment decoding of attention to spatially overlapped objects belonging to two different object categories. First, a whole-brain classifier was trained on pictures of faces and places. Subjects then saw transparently overlapped pictures of a face and a place, and attended to only one of them while ignoring the other. The category of the attended object, face or place, was decoded on a scan-by-scan basis using the previously trained decoder. The decoder performed at 77.6% accuracy indicating that despite competing bottom-up sensory input, object-based visual attention biased neural patterns towards that of the attended object. Furthermore, a comparison between different classification approaches indicated that the representation of faces and places is distributed rather than focal. This implies that real-time decoding of object-based attention requires a multivariate decoding approach that can detect these distributed patterns of cortical activity. © 2013 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.
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...
Partially blind instantly decodable network codes for lossy feedback environment
Sorour, Sameh; Douik, Ahmed S.; Valaee, Shahrokh; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim
2014-01-01
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
Directory of Open Access Journals (Sweden)
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
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.
Decoding English Alphabet Letters Using EEG Phase Information
Directory of Open Access Journals (Sweden)
YiYan Wang
2018-02-01
Full Text Available Increasing evidence indicates that the phase pattern and power of the low frequency oscillations of brain electroencephalograms (EEG contain significant information during the human cognition of sensory signals such as auditory and visual stimuli. Here, we investigate whether and how the letters of the alphabet can be directly decoded from EEG phase and power data. In addition, we investigate how different band oscillations contribute to the classification and determine the critical time periods. An English letter recognition task was assigned, and statistical analyses were conducted to decode the EEG signal corresponding to each letter visualized on a computer screen. We applied support vector machine (SVM with gradient descent method to learn the potential features for classification. It was observed that the EEG phase signals have a higher decoding accuracy than the oscillation power information. Low-frequency theta and alpha oscillations have phase information with higher accuracy than do other bands. The decoding performance was best when the analysis period began from 180 to 380 ms after stimulus presentation, especially in the lateral occipital and posterior temporal scalp regions (PO7 and PO8. These results may provide a new approach for brain-computer interface techniques (BCI and may deepen our understanding of EEG oscillations in cognition.
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...
Gold, Laura S; Klein, Gregory; Carr, Lauren; Kessler, Larry; Sullivan, Sean D
2012-01-25
In this article, we trace the chronology of developments in breast imaging technologies that are used for diagnosis and staging of breast cancer, including mammography, ultrasonography, magnetic resonance imaging, computed tomography, and positron emission tomography. We explore factors that affected clinical acceptance and utilization of these technologies from discovery to clinical use, including milestones in peer-reviewed publication, US Food and Drug Administration approval, reimbursement by payers, and adoption into clinical guidelines. The factors driving utilization of new imaging technologies are mainly driven by regulatory approval and reimbursement by payers rather than evidence that they provide benefits to patients. Comparative effectiveness research can serve as a useful tool to investigate whether these imaging modalities provide information that improves patient outcomes in real-world settings.
Multiple-Symbol Decision-Feedback Space-Time Differential Decoding in Fading Channels
Directory of Open Access Journals (Sweden)
Wang Xiaodong
2002-01-01
Full Text Available Space-time differential coding (STDC is an effective technique for exploiting transmitter diversity while it does not require the channel state information at the receiver. However, like conventional differential modulation schemes, it exhibits an error floor in fading channels. In this paper, we develop an STDC decoding technique based on multiple-symbol detection and decision-feedback, which makes use of the second-order statistic of the fading processes and has a very low computational complexity. This decoding method can significantly lower the error floor of the conventional STDC decoding algorithm, especially in fast fading channels. The application of the proposed multiple-symbol decision-feedback STDC decoding technique in orthogonal frequency-division multiplexing (OFDM system is also discussed.
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....
Decoding LDPC Convolutional Codes on Markov Channels
Directory of Open Access Journals (Sweden)
Kashyap Manohar
2008-01-01
Full Text Available Abstract This paper describes a pipelined iterative technique for joint decoding and channel state estimation of LDPC convolutional codes over Markov channels. Example designs are presented for the Gilbert-Elliott discrete channel model. We also compare the performance and complexity of our algorithm against joint decoding and state estimation of conventional LDPC block codes. Complexity analysis reveals that our pipelined algorithm reduces the number of operations per time step compared to LDPC block codes, at the expense of increased memory and latency. This tradeoff is favorable for low-power applications.
Decoding LDPC Convolutional Codes on Markov Channels
Directory of Open Access Journals (Sweden)
Chris Winstead
2008-04-01
Full Text Available This paper describes a pipelined iterative technique for joint decoding and channel state estimation of LDPC convolutional codes over Markov channels. Example designs are presented for the Gilbert-Elliott discrete channel model. We also compare the performance and complexity of our algorithm against joint decoding and state estimation of conventional LDPC block codes. Complexity analysis reveals that our pipelined algorithm reduces the number of operations per time step compared to LDPC block codes, at the expense of increased memory and latency. This tradeoff is favorable for low-power applications.
Toward a universal decoder of linguistic meaning from brain activation.
Pereira, Francisco; Lou, Bin; Pritchett, Brianna; Ritter, Samuel; Gershman, Samuel J; Kanwisher, Nancy; Botvinick, Matthew; Fedorenko, Evelina
2018-03-06
Prior work decoding linguistic meaning from imaging data has been largely limited to concrete nouns, using similar stimuli for training and testing, from a relatively small number of semantic categories. Here we present a new approach for building a brain decoding system in which words and sentences are represented as vectors in a semantic space constructed from massive text corpora. By efficiently sampling this space to select training stimuli shown to subjects, we maximize the ability to generalize to new meanings from limited imaging data. To validate this approach, we train the system on imaging data of individual concepts, and show it can decode semantic vector representations from imaging data of sentences about a wide variety of both concrete and abstract topics from two separate datasets. These decoded representations are sufficiently detailed to distinguish even semantically similar sentences, and to capture the similarity structure of meaning relationships between sentences.
A Parallel Decoding Algorithm for Short Polar Codes Based on Error Checking and Correcting
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
Dilemmas of compliance in the CIS
International Nuclear Information System (INIS)
Vorobyev, A.
1996-01-01
The objective of this paper is to examine some of the difficulties faced by Russia and other Common Independent States (CIS) in the field of compliance with disarmament treaties and non-proliferation regimes, as well as ways and means, particularly with regard to the legal framework, designed to overcome these difficulties. Naturally, the fate and pace of overcoming the existing problems will depend only partially on development of CIS States. A large variety of international factors and the general security will be essential for progress in resolving disarmament and arms control issues in the CIS
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....... in the well-know Gallager B algorithm, and increasing the output alphabet from hard decisions to two bits yields a gain of more than 1.0 dB in the required signal to noise ratio when using optimized codes. The code optimization requires adapting the mixing property of EXIT functions to the case of binary...
Directory of Open Access Journals (Sweden)
Je-Hyuk Lee
2009-11-01
Full Text Available Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We show that our approach to mapping cis-regulatory variants reduces in vitro experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells.
An overview of turbo decoding on fading channels
ATILGAN, Doğan
2009-01-01
A review of turbo coding and decoding has been presented in the literature [1]. In that paper, turbo coding and decoding on AWGN (Additive White Gaussian Noise) channels has been elaborated. In wireless communications, a phenomennon called multipath fading is frequently encountered. Therefore, investigation of efficient techniques to tackle with the destructive effects of fading is essential. Turbo coding has been proven as an efficient channel coding technique for AWGN channels. Some of the ...
Design and Analysis of Adaptive Message Coding on LDPC Decoder with Faulty Storage
Directory of Open Access Journals (Sweden)
Guangjun Ge
2018-01-01
Full Text Available Unreliable message storage severely degrades the performance of LDPC decoders. This paper discusses the impacts of message errors on LDPC decoders and schemes improving the robustness. Firstly, we develop a discrete density evolution analysis for faulty LDPC decoders, which indicates that protecting the sign bits of messages is effective enough for finite-precision LDPC decoders. Secondly, we analyze the effects of quantization precision loss for static sign bit protection and propose an embedded dynamic coding scheme by adaptively employing the least significant bits (LSBs to protect the sign bits. Thirdly, we give a construction of Hamming product code for the adaptive coding and present low complexity decoding algorithms. Theoretic analysis indicates that the proposed scheme outperforms traditional triple modular redundancy (TMR scheme in decoding both threshold and residual errors, while Monte Carlo simulations show that the performance loss is less than 0.2 dB when the storage error probability varies from 10-3 to 10-4.
Vectorization of Reed Solomon decoding and mapping on the EVP
Kumar, A.; Berkel, van C.H.
2008-01-01
Reed Solomon (RS) codes are used in a variety of (wireless) communication systems. Although commonly implemented in dedicated hardware, this paper explores the mapping of high-throughput RS decoding on vector DSPs. The four modules of such a decoder, viz. Syndrome Computation, Key Equation Solver,
Efficient decoding with steady-state Kalman filter in neural interface systems.
Malik, Wasim Q; Truccolo, Wilson; Brown, Emery N; Hochberg, Leigh R
2011-02-01
The Kalman filter is commonly used in neural interface systems to decode neural activity and estimate the desired movement kinematics. We analyze a low-complexity Kalman filter implementation in which the filter gain is approximated by its steady-state form, computed offline before real-time decoding commences. We evaluate its performance using human motor cortical spike train data obtained from an intracortical recording array as part of an ongoing pilot clinical trial. We demonstrate that the standard Kalman filter gain converges to within 95% of the steady-state filter gain in 1.5±0.5 s (mean ±s.d.). The difference in the intended movement velocity decoded by the two filters vanishes within 5 s, with a correlation coefficient of 0.99 between the two decoded velocities over the session length. We also find that the steady-state Kalman filter reduces the computational load (algorithm execution time) for decoding the firing rates of 25±3 single units by a factor of 7.0±0.9. We expect that the gain in computational efficiency will be much higher in systems with larger neural ensembles. The steady-state filter can thus provide substantial runtime efficiency at little cost in terms of estimation accuracy. This far more efficient neural decoding approach will facilitate the practical implementation of future large-dimensional, multisignal neural interface systems.
International Nuclear Information System (INIS)
Grey, C.A.
1994-01-01
A picture is drawn of the current supply side of the front-end fuel cycle production capacities in the CIS. Uranium production has been steadily declining, as in the West. Market realities have been reflected in local costs of production since the break-up of the former Soviet Union and some uneconomic mines have been closed. In terms of actual production, Kazakhstan, Russia and Uzbekistan, remain among the top five uranium producers in the world. Western government action has been taken to restrict the market access for natural uranium from the CIS. Reactors in the CIS continue to be supplied with fabricated fuel solely by Russian, though Western fuel fabricators have reduced Russian supplies to Eastern Europe. Russia's current dominance in conversion and enrichment services in both the CIS and Eastern Europe is likely to continue as long as the present surplus low enriched uranium stocks last and surplus production capacity exists. Market penetration in the West has been limited by government action but Russia in 1993 still held about 20% of the world's conversion market and nearly 19% of the enrichment market. (6 figures, 2 tables, 4 references) (UK)
Effect of video decoder errors on video interpretability
Young, Darrell L.
2014-06-01
The advancement in video compression technology can result in more sensitivity to bit errors. Bit errors can propagate causing sustained loss of interpretability. In the worst case, the decoder "freezes" until it can re-synchronize with the stream. Detection of artifacts enables downstream processes to avoid corrupted frames. A simple template approach to detect block stripes and a more advanced cascade approach to detect compression artifacts was shown to correlate to the presence of artifacts and decoder messages.
Parallel iterative decoding of transform domain Wyner-Ziv video using cross bitplane correlation
DEFF Research Database (Denmark)
Luong, Huynh Van; Huang, Xin; Forchhammer, Søren
2011-01-01
decoding scheme is proposed to improve the coding efficiency of TDWZ video codecs. The proposed parallel iterative LDPC decoding scheme is able to utilize cross bitplane correlation during decoding, by iteratively refining the soft-input, updating a modeled noise distribution and thereafter enhancing......In recent years, Transform Domain Wyner-Ziv (TDWZ) video coding has been proposed as an efficient Distributed Video Coding (DVC) solution, which fully or partly exploits the source statistics at the decoder to reduce the computational burden at the encoder. In this paper, a parallel iterative LDPC...
Decoding bipedal locomotion from the rat sensorimotor cortex
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
The fast decoding of Reed-Solomon codes using Fermat theoretic transforms and continued fractions
Reed, I. S.; Scholtz, R. A.; Welch, L. R.; Truong, T. K.
1978-01-01
It is shown that Reed-Solomon (RS) codes can be decoded by using a fast Fourier transform (FFT) algorithm over finite fields GF(F sub n), where F sub n is a Fermat prime, and continued fractions. This new transform decoding method is simpler than the standard method for RS codes. The computing time of this new decoding algorithm in software can be faster than the standard decoding method for RS codes.
International Nuclear Information System (INIS)
Yang, P.; Aglieri, G.; Cavicchioli, C.; Chalmet, P.L.; Chanlek, N.; Collu, A.; Gao, C.; Hillemanns, H.; Junique, A.; Kofarago, M.; Keil, M.; Kugathasan, T.; Kim, D.; Kim, J.; Lattuca, A.; Marin Tobon, C.A.; Marras, D.; Mager, M.; Martinengo, P.; Mazza, G.
2015-01-01
Active Pixel Sensors used in High Energy Particle Physics require low power consumption to reduce the detector material budget, low integration time to reduce the possibilities of pile-up and fast readout to improve the detector data capability. To satisfy these requirements, a novel Address-Encoder and Reset-Decoder (AERD) asynchronous circuit for a fast readout of a pixel matrix has been developed. The AERD data-driven readout architecture operates the address encoding and reset decoding based on an arbitration tree, and allows us to readout only the hit pixels. Compared to the traditional readout structure of the rolling shutter scheme in Monolithic Active Pixel Sensors (MAPS), AERD can achieve a low readout time and a low power consumption especially for low hit occupancies. The readout is controlled at the chip periphery with a signal synchronous with the clock, allows a good digital and analogue signal separation in the matrix and a reduction of the power consumption. The AERD circuit has been implemented in the TowerJazz 180 nm CMOS Imaging Sensor (CIS) process with full complementary CMOS logic in the pixel. It works at 10 MHz with a matrix height of 15 mm. The energy consumed to read out one pixel is around 72 pJ. A scheme to boost the readout speed to 40 MHz is also discussed. The sensor chip equipped with AERD has been produced and characterised. Test results including electrical beam measurement are presented
Energy Technology Data Exchange (ETDEWEB)
Yang, P., E-mail: yangping0710@126.com [Central China Normal University, Wuhan (China); Aglieri, G.; Cavicchioli, C. [CERN, 1210 Geneva 23 (Switzerland); Chalmet, P.L. [MIND, Archamps (France); Chanlek, N. [Suranaree University of Technology, Nakhon Ratchasima (Thailand); Collu, A. [University of Cagliari, Cagliari (Italy); INFN (Italy); Gao, C. [Central China Normal University, Wuhan (China); Hillemanns, H.; Junique, A. [CERN, 1210 Geneva 23 (Switzerland); Kofarago, M. [CERN, 1210 Geneva 23 (Switzerland); University of Utrecht, Utrecht (Netherlands); Keil, M.; Kugathasan, T. [CERN, 1210 Geneva 23 (Switzerland); Kim, D. [Dongguk and Yonsei University, Seoul (Korea, Republic of); Kim, J. [Pusan National University, Busan (Korea, Republic of); Lattuca, A. [University of Torino, Torino (Italy); INFN (Italy); Marin Tobon, C.A. [CERN, 1210 Geneva 23 (Switzerland); Marras, D. [University of Cagliari, Cagliari (Italy); INFN (Italy); Mager, M.; Martinengo, P. [CERN, 1210 Geneva 23 (Switzerland); Mazza, G. [University of Torino, Torino (Italy); INFN (Italy); and others
2015-06-11
Active Pixel Sensors used in High Energy Particle Physics require low power consumption to reduce the detector material budget, low integration time to reduce the possibilities of pile-up and fast readout to improve the detector data capability. To satisfy these requirements, a novel Address-Encoder and Reset-Decoder (AERD) asynchronous circuit for a fast readout of a pixel matrix has been developed. The AERD data-driven readout architecture operates the address encoding and reset decoding based on an arbitration tree, and allows us to readout only the hit pixels. Compared to the traditional readout structure of the rolling shutter scheme in Monolithic Active Pixel Sensors (MAPS), AERD can achieve a low readout time and a low power consumption especially for low hit occupancies. The readout is controlled at the chip periphery with a signal synchronous with the clock, allows a good digital and analogue signal separation in the matrix and a reduction of the power consumption. The AERD circuit has been implemented in the TowerJazz 180 nm CMOS Imaging Sensor (CIS) process with full complementary CMOS logic in the pixel. It works at 10 MHz with a matrix height of 15 mm. The energy consumed to read out one pixel is around 72 pJ. A scheme to boost the readout speed to 40 MHz is also discussed. The sensor chip equipped with AERD has been produced and characterised. Test results including electrical beam measurement are presented.
Yang, P.; Aglieri, G.; Cavicchioli, C.; Chalmet, P. L.; Chanlek, N.; Collu, A.; Gao, C.; Hillemanns, H.; Junique, A.; Kofarago, M.; Keil, M.; Kugathasan, T.; Kim, D.; Kim, J.; Lattuca, A.; Marin Tobon, C. A.; Marras, D.; Mager, M.; Martinengo, P.; Mazza, G.; Mugnier, H.; Musa, L.; Puggioni, C.; Rousset, J.; Reidt, F.; Riedler, P.; Snoeys, W.; Siddhanta, S.; Usai, G.; van Hoorne, J. W.; Yi, J.
2015-06-01
Active Pixel Sensors used in High Energy Particle Physics require low power consumption to reduce the detector material budget, low integration time to reduce the possibilities of pile-up and fast readout to improve the detector data capability. To satisfy these requirements, a novel Address-Encoder and Reset-Decoder (AERD) asynchronous circuit for a fast readout of a pixel matrix has been developed. The AERD data-driven readout architecture operates the address encoding and reset decoding based on an arbitration tree, and allows us to readout only the hit pixels. Compared to the traditional readout structure of the rolling shutter scheme in Monolithic Active Pixel Sensors (MAPS), AERD can achieve a low readout time and a low power consumption especially for low hit occupancies. The readout is controlled at the chip periphery with a signal synchronous with the clock, allows a good digital and analogue signal separation in the matrix and a reduction of the power consumption. The AERD circuit has been implemented in the TowerJazz 180 nm CMOS Imaging Sensor (CIS) process with full complementary CMOS logic in the pixel. It works at 10 MHz with a matrix height of 15 mm. The energy consumed to read out one pixel is around 72 pJ. A scheme to boost the readout speed to 40 MHz is also discussed. The sensor chip equipped with AERD has been produced and characterised. Test results including electrical beam measurement are presented.
Clusterless Decoding of Position From Multiunit Activity Using A Marked Point Process Filter
Deng, Xinyi; Liu, Daniel F.; Kay, Kenneth; Frank, Loren M.; Eden, Uri T.
2016-01-01
Point process filters have been applied successfully to decode neural signals and track neural dynamics. Traditionally, these methods assume that multiunit spiking activity has already been correctly spike-sorted. As a result, these methods are not appropriate for situations where sorting cannot be performed with high precision such as real-time decoding for brain-computer interfaces. As the unsupervised spike-sorting problem remains unsolved, we took an alternative approach that takes advantage of recent insights about clusterless decoding. Here we present a new point process decoding algorithm that does not require multiunit signals to be sorted into individual units. We use the theory of marked point processes to construct a function that characterizes the relationship between a covariate of interest (in this case, the location of a rat on a track) and features of the spike waveforms. In our example, we use tetrode recordings, and the marks represent a four-dimensional vector of the maximum amplitudes of the spike waveform on each of the four electrodes. In general, the marks may represent any features of the spike waveform. We then use Bayes’ rule to estimate spatial location from hippocampal neural activity. We validate our approach with a simulation study and with experimental data recorded in the hippocampus of a rat moving through a linear environment. Our decoding algorithm accurately reconstructs the rat’s position from unsorted multiunit spiking activity. We then compare the quality of our decoding algorithm to that of a traditional spike-sorting and decoding algorithm. Our analyses show that the proposed decoding algorithm performs equivalently or better than algorithms based on sorted single-unit activity. These results provide a path toward accurate real-time decoding of spiking patterns that could be used to carry out content-specific manipulations of population activity in hippocampus or elsewhere in the brain. PMID:25973549
Complexity Analysis of Reed-Solomon Decoding over GF(2m without Using Syndromes
Directory of Open Access Journals (Sweden)
Zhiyuan Yan
2008-06-01
Full Text Available There has been renewed interest in decoding Reed-Solomon (RS codes without using syndromes recently. In this paper, we investigate the complexity of syndromeless decoding, and compare it to that of syndrome-based decoding. Aiming to provide guidelines to practical applications, our complexity analysis focuses on RS codes over characteristic-2 fields, for which some multiplicative FFT techniques are not applicable. Due to moderate block lengths of RS codes in practice, our analysis is complete, without big O notation. In addition to fast implementation using additive FFT techniques, we also consider direct implementation, which is still relevant for RS codes with moderate lengths. For high-rate RS codes, when compared to syndrome-based decoding algorithms, not only syndromeless decoding algorithms require more field operations regardless of implementation, but also decoder architectures based on their direct implementations have higher hardware costs and lower throughput. We also derive tighter bounds on the complexities of fast polynomial multiplications based on Cantor's approach and the fast extended Euclidean algorithm.
A lossy graph model for delay reduction in generalized instantly decodable network coding
Douik, Ahmed S.
2014-06-01
The problem of minimizing the decoding delay in Generalized instantly decodable network coding (G-IDNC) for both perfect and lossy feedback scenarios is formulated as a maximum weight clique problem over the G-IDNC graph in. In this letter, we introduce a new lossy G-IDNC graph (LG-IDNC) model to further minimize the decoding delay in lossy feedback scenarios. Whereas the G-IDNC graph represents only doubtless combinable packets, the LG-IDNC graph represents also uncertain packet combinations, arising from lossy feedback events, when the expected decoding delay of XORing them among themselves or with other certain packets is lower than that expected when sending these packets separately. We compare the decoding delay performance of LG-IDNC and G-IDNC graphs through extensive simulations. Numerical results show that our new LG-IDNC graph formulation outperforms the G-IDNC graph formulation in all lossy feedback situations and achieves significant improvement in the decoding delay especially when the feedback erasure probability is higher than the packet erasure probability. © 2012 IEEE.
Decoding Dyslexia, a Common Learning Disability
... if they continue to struggle. Read More "Dyslexic" Articles In Their Own Words: Dealing with Dyslexia / Decoding Dyslexia, a Common Learning Disability / What is Dyslexia? / Special Education and Research ...
Characterization of noncoding regulatory DNA in the human genome.
Elkon, Ran; Agami, Reuven
2017-08-08
Genetic variants associated with common diseases are usually located in noncoding parts of the human genome. Delineation of the full repertoire of functional noncoding elements, together with efficient methods for probing their biological roles, is therefore of crucial importance. Over the past decade, DNA accessibility and various epigenetic modifications have been associated with regulatory functions. Mapping these features across the genome has enabled researchers to begin to document the full complement of putative regulatory elements. High-throughput reporter assays to probe the functions of regulatory regions have also been developed but these methods separate putative regulatory elements from the chromosome so that any effects of chromatin context and long-range regulatory interactions are lost. Definitive assignment of function(s) to putative cis-regulatory elements requires perturbation of these elements. Genome-editing technologies are now transforming our ability to perturb regulatory elements across entire genomes. Interpretation of high-throughput genetic screens that incorporate genome editors might enable the construction of an unbiased map of functional noncoding elements in the human genome.
A Fully Parallel VLSI-implementation of the Viterbi Decoding Algorithm
DEFF Research Database (Denmark)
Sparsø, Jens; Jørgensen, Henrik Nordtorp; Paaske, Erik
1989-01-01
In this paper we describe the implementation of a K = 7, R = 1/2 single-chip Viterbi decoder intended to operate at 10-20 Mbit/sec. We propose a general, regular and area efficient floor-plan that is also suitable for implementation of decoders for codes with different generator polynomials...
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...
Word Decoding Development during Phonics Instruction in Children at Risk for Dyslexia.
Schaars, Moniek M H; Segers, Eliane; Verhoeven, Ludo
2017-05-01
In the present study, we examined the early word decoding development of 73 children at genetic risk of dyslexia and 73 matched controls. We conducted monthly curriculum-embedded word decoding measures during the first 5 months of phonics-based reading instruction followed by standardized word decoding measures halfway and by the end of first grade. In kindergarten, vocabulary, phonological awareness, lexical retrieval, and verbal and visual short-term memory were assessed. The results showed that the children at risk were less skilled in phonemic awareness in kindergarten. During the first 5 months of reading instruction, children at risk were less efficient in word decoding and the discrepancy increased over the months. In subsequent months, the discrepancy prevailed for simple words but increased for more complex words. Phonemic awareness and lexical retrieval predicted the reading development in children at risk and controls to the same extent. It is concluded that children at risk are behind their typical peers in word decoding development starting from the very beginning. Furthermore, it is concluded that the disadvantage increased during phonics instruction and that the same predictors underlie the development of word decoding in the two groups of children. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.
Min-Max decoding for non binary LDPC codes
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 c...
Indian Academy of Sciences (India)
Shannon limit of the channel. Among the earliest discovered codes that approach the. Shannon limit were the low density parity check (LDPC) codes. The term low density arises from the property of the parity check matrix defining the code. We will now define this matrix and the role that it plays in decoding. 2. Linear Codes.
Liu, K. Y.
1986-01-01
High-speed decoder intended for use with Reed-Solomon (RS) codes of long code length and high error-correcting capability. Design based on algorithm that includes high-radix Fermat transform procedure, which is most efficient for high speeds. RS code in question has code-word length of 256 symbols, of which 224 are information symbols and 32 are redundant.
The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb
Cotney, Justin; Leng, Jing; Yin, Jun; Reilly, Steven K.; DeMare, Laura E.; Emera, Deena; Ayoub, Albert E.; Rakic, Pasko; Noonan, James P.
2013-01-01
The evolution of human anatomical features likely involved changes in gene regulation during development. However, the nature and extent of human-specific developmental regulatory functions remain unknown. We obtained a genome-wide view of cis-regulatory evolution in human embryonic tissues by comparing the histone modification H3K27ac, which provides a quantitative readout of promoter and enhancer activity, during human, rhesus, and mouse limb development. Based on increased H3K27ac, we find...
Prior Knowledge Improves Decoding of Finger Flexion from Electrocorticographic (ECoG Signals
Directory of Open Access Journals (Sweden)
Zuoguan eWang
2011-11-01
Full Text Available Brain-computer interfaces (BCIs use brain signals to convey a user's intent. Some BCI approaches begin by decoding kinematic parameters of movements from brain signals, and then proceed to using these signals, in absence of movements, to allow a user to control an output. Recent results have shown that electrocorticographic (ECoG recordings from the surface of the brain in humans can give information about kinematic parameters (eg{} hand velocity or finger flexion. The decoding approaches in these studies usually employed classical classification/regression algorithms that derive a linear mapping between brain signals and outputs. However, they typically only incorporate little prior information about the target movement parameter. In this paper, we incorporate prior knowledge using a Bayesian decoding method, and use it to decode finger flexion from ECoG signals. Specifically, we exploit the anatomic constraints and dynamic constraints that govern finger flexion and incorporate these constraints in the construction, structure, and the probabilistic functions of the prior model of a switched non-parametric dynamic system (SNDS. Given a measurement model resulting from a traditional linear regression method, we decoded finger flexion using posterior estimation that combined the prior and measurement models. Our results show that the application of the Bayesian decoding model, which incorporates prior knowledge, improves decoding performance compared to the application of a linear regression model, which does not incorporate prior knowledge. Thus, the results presented in this paper may ultimately lead to neurally controlled hand prostheses with full fine-grained finger articulation.
Role of Gender and Linguistic Diversity in Word Decoding Development
Verhoeven, Ludo; van Leeuwe, Jan
2011-01-01
The purpose of the present study was to investigate the role of gender and linguistic diversity in the growth of Dutch word decoding skills throughout elementary school for a representative sample of children living in the Netherlands. Following a longitudinal design, the children's decoding abilities for (1) regular CVC words, (2) complex…
Handore, Kishor L; Seetharamsingh, B; Reddy, D Srinivasa
2013-08-16
A simple and efficient synthesis of functionalized cis-hydrindanes and cis-decalins was achieved using a sequential Diels-Alder/aldol approach in a highly diastereoselective manner. The scope of this method was tested with a variety of substrates and was successfully applied to the synthesis of two natural products in racemic form. The highlights of the present work provide ready access to 13 new cis-hydrindanes/cis-decalins, a protecting group-free total synthesis of an insect repellent Nootkatone, and the first synthesis of a Noreremophilane using the shortest sequence.
A bidirectional brain-machine interface featuring a neuromorphic hardware decoder
Directory of Open Access Journals (Sweden)
Fabio Boi
2016-12-01
Full Text Available Bidirectional brain-machine interfaces (BMIs establish a two-way direct communication link4 between the brain and the external world. A decoder translates recorded neural activity into motor5 commands and an encoder delivers sensory information collected from the environment directly6 to the brain creating a closed-loop system. These two modules are typically integrated in bulky7 external devices. However, the clinical support of patients with severe motor and sensory deficits8 requires compact, low-power, and fully implantable systems that can decode neural signals to9 control external devices. As a first step toward this goal, we developed a modular bidirectional BMI10 setup that uses a compact neuromorphic processor as a decoder. On this chip we implemented11 a network of spiking neurons built using its ultra-low-power mixed-signal analog/digital circuits.12 On-chip on-line spike-timing-dependent plasticity synapse circuits enabled the network to learn13 to decode neural signals recorded from the brain into motor outputs controlling the movements14 of an external device. The modularity of the BMI allowed us to tune the individual components15 of the setup without modifying the whole system. In this paper we present the features of16 this modular BMI, and describe how we configured the network of spiking neuron circuits to17 implement the decoder and to coordinate it with the encoder in an experimental BMI paradigm18 that connects bidirectionally the brain of an anesthetized rat with an external object. We show that19 the chip learned the decoding task correctly, allowing the interfaced brain to control the object’s20 trajectories robustly. Based on our demonstration, we propose that neuromorphic technology is21 mature enough for the development of BMI modules that are sufficiently low-power and compact,22 while being highly computationally powerful and adaptive.
A Bidirectional Brain-Machine Interface Featuring a Neuromorphic Hardware Decoder.
Boi, Fabio; Moraitis, Timoleon; De Feo, Vito; Diotalevi, Francesco; Bartolozzi, Chiara; Indiveri, Giacomo; Vato, Alessandro
2016-01-01
Bidirectional brain-machine interfaces (BMIs) establish a two-way direct communication link between the brain and the external world. A decoder translates recorded neural activity into motor commands and an encoder delivers sensory information collected from the environment directly to the brain creating a closed-loop system. These two modules are typically integrated in bulky external devices. However, the clinical support of patients with severe motor and sensory deficits requires compact, low-power, and fully implantable systems that can decode neural signals to control external devices. As a first step toward this goal, we developed a modular bidirectional BMI setup that uses a compact neuromorphic processor as a decoder. On this chip we implemented a network of spiking neurons built using its ultra-low-power mixed-signal analog/digital circuits. On-chip on-line spike-timing-dependent plasticity synapse circuits enabled the network to learn to decode neural signals recorded from the brain into motor outputs controlling the movements of an external device. The modularity of the BMI allowed us to tune the individual components of the setup without modifying the whole system. In this paper, we present the features of this modular BMI and describe how we configured the network of spiking neuron circuits to implement the decoder and to coordinate it with the encoder in an experimental BMI paradigm that connects bidirectionally the brain of an anesthetized rat with an external object. We show that the chip learned the decoding task correctly, allowing the interfaced brain to control the object's trajectories robustly. Based on our demonstration, we propose that neuromorphic technology is mature enough for the development of BMI modules that are sufficiently low-power and compact, while being highly computationally powerful and adaptive.
Duuren, van J.B.J.H.
2011-01-01
Optimization of Pseudomonas putida KT2440 as host for the production of cis, cis-muconate
from benzoate P. putida KT2440 was used as biocatalyst given its versatile and energetically robust metabolism.
Therefore, a mutant was generated and a process developed based on which a
Peeling Decoding of LDPC Codes with Applications in Compressed Sensing
Directory of Open Access Journals (Sweden)
Weijun Zeng
2016-01-01
Full Text Available We present a new approach for the analysis of iterative peeling decoding recovery algorithms in the context of Low-Density Parity-Check (LDPC codes and compressed sensing. The iterative recovery algorithm is particularly interesting for its low measurement cost and low computational complexity. The asymptotic analysis can track the evolution of the fraction of unrecovered signal elements in each iteration, which is similar to the well-known density evolution analysis in the context of LDPC decoding algorithm. Our analysis shows that there exists a threshold on the density factor; if under this threshold, the recovery algorithm is successful; otherwise it will fail. Simulation results are also provided for verifying the agreement between the proposed asymptotic analysis and recovery algorithm. Compared with existing works of peeling decoding algorithm, focusing on the failure probability of the recovery algorithm, our proposed approach gives accurate evolution of performance with different parameters of measurement matrices and is easy to implement. We also show that the peeling decoding algorithm performs better than other schemes based on LDPC codes.
Markov source model for printed music decoding
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.
Seok, Junhee; Kaushal, Amit; Davis, Ronald W; Xiao, Wenzhong
2010-01-18
The large amount of high-throughput genomic data has facilitated the discovery of the regulatory relationships between transcription factors and their target genes. While early methods for discovery of transcriptional regulation relationships from microarray data often focused on the high-throughput experimental data alone, more recent approaches have explored the integration of external knowledge bases of gene interactions. In this work, we develop an algorithm that provides improved performance in the prediction of transcriptional regulatory relationships by supplementing the analysis of microarray data with a new method of integrating information from an existing knowledge base. Using a well-known dataset of yeast microarrays and the Yeast Proteome Database, a comprehensive collection of known information of yeast genes, we show that knowledge-based predictions demonstrate better sensitivity and specificity in inferring new transcriptional interactions than predictions from microarray data alone. We also show that comprehensive, direct and high-quality knowledge bases provide better prediction performance. Comparison of our results with ChIP-chip data and growth fitness data suggests that our predicted genome-wide regulatory pairs in yeast are reasonable candidates for follow-up biological verification. High quality, comprehensive, and direct knowledge bases, when combined with appropriate bioinformatic algorithms, can significantly improve the discovery of gene regulatory relationships from high throughput gene expression data.
DS-OCDMA Encoder/Decoder Performance Analysis Using Optical Low-Coherence Reflectometry
Fsaifes, Ihsan; Lepers, Catherine; Obaton, Anne-Francoise; Gallion, Philippe
2006-08-01
Direct-sequence optical code-division multiple-access (DS-OCDMA) encoder/decoder based on sampled fiber Bragg gratings (S-FBGs) is characterized using phase-sensitive optical low-coherence reflectometry (OLCR). The OLCR technique allows localized measurements of FBG wavelength and physical length inside one S-FBG. This paper shows how the discrepancies between specifications and measurements of the different FBGs have some impact on spectral and temporal pulse responses of the OCDMA encoder/decoder. The FBG physical lengths lower than the specified ones are shown to affect the mean optical power reflected by the OCDMA encoder/decoder. The FBG wavelengths that are detuned from each other induce some modulations of S-FBG reflectivity resulting in encoder/decoder sensitivity to laser wavelength drift of the OCDMA system. Finally, highlighted by this OLCR study, some solutions to overcome limitations in performance with the S-FBG technology are suggested.
Peter M Keller; Thomas J Richardson
2003-01-01
Monetary policy has become increasingly important in the countries of the Commonwealth of Independent States (CIS) as fiscal adjustment and structural reforms have taken root. Inflation has been brought down to relatively low levels in almost all of these countries, raising the question of what should be the appropriate nominal anchor at this stage. Formally, almost all CIS countries have floating exchange rate regimes, yet in practice they manage their exchange rates very heavily, perhaps be...
Kreiman, Gabriel
2004-01-01
Sequence information and high‐throughput methods to measure gene expression levels open the door to explore transcriptional regulation using computational tools. Combinatorial regulation and sparseness of regulatory elements throughout the genome allow organisms to control the spatial and temporal patterns of gene expression. Here we study the organization of cis‐regulatory elements in sets of co‐regulated genes. We build an algorithm to search for combinations of transcription factor binding...
IQ Predicts Word Decoding Skills in Populations with Intellectual Disabilities
Levy, Yonata
2011-01-01
This is a study of word decoding in adolescents with Down syndrome and in adolescents with Intellectual Deficits of unknown etiology. It was designed as a replication of studies of word decoding in English speaking and in Hebrew speaking adolescents with Williams syndrome ([0230] and [0235]). Participants' IQ was matched to IQ in the groups with…
Coder and decoder of fractal signals of comb-type structure
Directory of Open Access Journals (Sweden)
Politanskyi R. L.
2014-08-01
Full Text Available The article presents a coder and decoder of fractal signals of comb-type structure (FSCS based on microcontrollers (MC. The coder and decoder consist of identical control modules, while their managed modules have different schematic constructions. The control module performs forming or recognition of signals, and also carries out the function of information exchange with a computer. The basic element of the control module is a PIC18F2550 microcontroller from MicroChip. The coder of the system forms fractal signals of a given order according to the information bits coming from the computer. Samples of the calculated values of the amplitudes of elementary rectangular pulses that constitute the structure of fractal pulses are stored in the memory of the microcontroller as a table. Minimum bit capacity of the DAC necessary for the generation of FSCS of fourth order is four bits. The operation algorithm, "wired" into the controller of the program, provides for encoding of the transmitted information by two-bit symbols. Recognition of the start of transmission of each byte in communication channel is performed by the transmission of the timing signal. In a decoder the microcontroller carries out reception and decoding of the received fractal signals which are then transmitted to the computer. The developed algorithm of the program for the microcontroller of the decoder is carried out by determination of order of fractal impulse after the value of sum of amplitudes of elementary impulses, constituents fractal signal. The programs for coder and decoder are written in "C". In the most critical places of the program influencing on the fast-acting of chart “assembler” insertions are done. The blocks of the coder and decoder were connected with a coaxial 10 meters long cable with an impendance of 75 Ohm. The signals generated by the developed coder of FSCS, were studied using a digital oscillograph. On the basis of the obtained spectrums, it is possible
Decoding DNA labels by melting curve analysis using real-time PCR.
Balog, József A; Fehér, Liliána Z; Puskás, László G
2017-12-01
Synthetic DNA has been used as an authentication code for a diverse number of applications. However, existing decoding approaches are based on either DNA sequencing or the determination of DNA length variations. Here, we present a simple alternative protocol for labeling different objects using a small number of short DNA sequences that differ in their melting points. Code amplification and decoding can be done in two steps using quantitative PCR (qPCR). To obtain a DNA barcode with high complexity, we defined 8 template groups, each having 4 different DNA templates, yielding 158 (>2.5 billion) combinations of different individual melting temperature (Tm) values and corresponding ID codes. The reproducibility and specificity of the decoding was confirmed by using the most complex template mixture, which had 32 different products in 8 groups with different Tm values. The industrial applicability of our protocol was also demonstrated by labeling a drone with an oil-based paint containing a predefined DNA code, which was then successfully decoded. The method presented here consists of a simple code system based on a small number of synthetic DNA sequences and a cost-effective, rapid decoding protocol using a few qPCR reactions, enabling a wide range of authentication applications.
Mirkovic, Bojana; Debener, Stefan; Jaeger, Manuela; De Vos, Maarten
2015-08-01
Objective. Recent studies have provided evidence that temporal envelope driven speech decoding from high-density electroencephalography (EEG) and magnetoencephalography recordings can identify the attended speech stream in a multi-speaker scenario. The present work replicated the previous high density EEG study and investigated the necessary technical requirements for practical attended speech decoding with EEG. Approach. Twelve normal hearing participants attended to one out of two simultaneously presented audiobook stories, while high density EEG was recorded. An offline iterative procedure eliminating those channels contributing the least to decoding provided insight into the necessary channel number and optimal cross-subject channel configuration. Aiming towards the future goal of near real-time classification with an individually trained decoder, the minimum duration of training data necessary for successful classification was determined by using a chronological cross-validation approach. Main results. Close replication of the previously reported results confirmed the method robustness. Decoder performance remained stable from 96 channels down to 25. Furthermore, for less than 15 min of training data, the subject-independent (pre-trained) decoder performed better than an individually trained decoder did. Significance. Our study complements previous research and provides information suggesting that efficient low-density EEG online decoding is within reach.
Fleisher, Linda; Wen, Kuang Yi; Miller, Suzanne M; Diefenbach, Michael; Stanton, Annette L; Ropka, Mary; Morra, Marion; Raich, Peter C
2015-11-01
Cancer patients and survivors are assuming active roles in decision-making and digital patient support tools are widely used to facilitate patient engagement. As part of Cancer Information Service Research Consortium's randomized controlled trials focused on the efficacy of eHealth interventions to promote informed treatment decision-making for newly diagnosed prostate and breast cancer patients, and post-treatment breast cancer, we conducted a rigorous process evaluation to examine the actual use of and perceived benefits of two complementary communication channels -- print and eHealth interventions. The three Virtual Cancer Information Service (V-CIS) interventions were developed through a rigorous developmental process, guided by self-regulatory theory, informed decision-making frameworks, and health communications best practices. Control arm participants received NCI print materials; experimental arm participants received the additional V-CIS patient support tool. Actual usage data from the web-based V-CIS was also obtained and reported. Print materials were highly used by all groups. About 60% of the experimental group reported using the V-CIS. Those who did use the V-CIS rated it highly on improvements in knowledge, patient-provider communication and decision-making. The findings show that how patients actually use eHealth interventions either singularly or within the context of other communication channels is complex. Integrating rigorous best practices and theoretical foundations is essential and multiple communication approaches should be considered to support patient preferences.
The basis of orientation decoding in human primary visual cortex: fine- or coarse-scale biases?
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.
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....
A new LDPC decoding scheme for PDM-8QAM BICM coherent optical communication system
Liu, Yi; Zhang, Wen-bo; Xi, Li-xia; Tang, Xian-feng; Zhang, Xiao-guang
2015-11-01
A new log-likelihood ratio (LLR) message estimation method is proposed for polarization-division multiplexing eight quadrature amplitude modulation (PDM-8QAM) bit-interleaved coded modulation (BICM) optical communication system. The formulation of the posterior probability is theoretically analyzed, and the way to reduce the pre-decoding bit error rate ( BER) of the low density parity check (LDPC) decoder for PDM-8QAM constellations is presented. Simulation results show that it outperforms the traditional scheme, i.e., the new post-decoding BER is decreased down to 50% of that of the traditional post-decoding algorithm.
Network perturbation by recurrent regulatory variants in cancer.
Directory of Open Access Journals (Sweden)
Kiwon Jang
2017-03-01
Full Text Available Cancer driving genes have been identified as recurrently affected by variants that alter protein-coding sequences. However, a majority of cancer variants arise in noncoding regions, and some of them are thought to play a critical role through transcriptional perturbation. Here we identified putative transcriptional driver genes based on combinatorial variant recurrence in cis-regulatory regions. The identified genes showed high connectivity in the cancer type-specific transcription regulatory network, with high outdegree and many downstream genes, highlighting their causative role during tumorigenesis. In the protein interactome, the identified transcriptional drivers were not as highly connected as coding driver genes but appeared to form a network module centered on the coding drivers. The coding and regulatory variants associated via these interactions between the coding and transcriptional drivers showed exclusive and complementary occurrence patterns across tumor samples. Transcriptional cancer drivers may act through an extensive perturbation of the regulatory network and by altering protein network modules through interactions with coding driver genes.
Davidi, Lital; Pick, Uri
2017-06-01
We identified and demonstrated the function of 9-cis/all-trans β-carotene isomerases in plastidic globules of Dunaliella bardawil, the species accumulating the highest levels of 9-cis β-carotene that is essential for humans. The halotolerant alga Dunaliella bardawil is unique in that it accumulates under light stress high levels of β-carotene in plastidic lipid globules. The pigment is composed of two major isomers: all-trans β-carotene, the common natural form of this pigment, and 9-cis β-carotene. The biosynthetic pathway of β-carotene is known, but it is not clear how the 9-cis isomer is formed. We identified in plastidic lipid globules that were isolated from D. bardawil two proteins with high sequence homology to the D27 protein-a 9-cis/all-trans β-carotene isomerase from rice (Alder et al. Science 335:1348-1351, 2012). The proteins are enriched in the oil globules by 6- to 17-fold compared to chloroplast proteins. The expression of the corresponding genes, 9-cis-βC-iso1 and 9-cis-βC-iso2, is enhanced under light stress. The synthetic proteins catalyze in vitro conversion of all-trans to 9-cis β-carotene. Expression of the 9-cis-βC-iso1 or of 9-cis-βC-iso2 genes in an E. coli mutant line that harbors β-carotene biosynthesis genes enhanced the conversion of all-trans into 9-cis β-carotene. These results suggest that 9-cis-βC-ISO1 and 9-cis-βC-ISO2 proteins are responsible for the formation of 9-cis β-carotene in D. bardawil under stress conditions.
Studies on radiosensitization of Escherichia coli cells by cis-platinum complexes
International Nuclear Information System (INIS)
Zimbrick, J.D.; Sukrochana, A.; Richmond, R.C.
1979-01-01
We recently reported that the antitumor drug cis-Pt(NH 3 ) 2 Cl 2 (cis-DDP) produces significant radiosensitization of anoxic E coli C cells. We have extended these studies to three other platinum drugs, all of which have been shown to be more effective antitumor drugs than cis-DDP. The drugs are: cis-dichloro bis(ethylene imine) Pt(II) (cis-DEP); cis-dichlorobicyclopentylamine Pt(II) (cis-PAD); and Pt-thymine blue (cis-PTB). Survival curve studies indicate that these drugs all produce greater anoxic radiosensitization of E coli C than cis-DDP at concentrations which are less toxic to the cells than similar concentrations of cis-DDP. If the cells are treated with any one of these drugs for two hours and then washed to remove the drug before irradiation, no detectable radiosensitization is found. We conclude that these drugs have the potential for being useful agents in combined modality therapy and that they warrant further study in mammalian systems
Directory of Open Access Journals (Sweden)
Jennifer Yihong Tan
2017-02-01
Full Text Available Summary: Intergenic long noncoding RNAs (lincRNAs are the largest class of transcripts in the human genome. Although many have recently been linked to complex human traits, the underlying mechanisms for most of these transcripts remain undetermined. We investigated the regulatory roles of a high-confidence and reproducible set of 69 trait-relevant lincRNAs (TR-lincRNAs in human lymphoblastoid cells whose biological relevance is supported by their evolutionary conservation during recent human history and genetic interactions with other trait-associated loci. Their enrichment in enhancer-like chromatin signatures, interactions with nearby trait-relevant protein-coding loci, and preferential location at topologically associated domain (TAD boundaries provide evidence that TR-lincRNAs likely regulate proximal trait-relevant gene expression in cis by modulating local chromosomal architecture. This is consistent with the positive and significant correlation found between TR-lincRNA abundance and intra-TAD DNA-DNA contacts. Our results provide insights into the molecular mode of action by which TR-lincRNAs contribute to complex human traits. : Tan et al. identify and characterize 69 human complex trait/disease-associated lincRNAs in LCLs. They show that these loci are often associated with cis-regulation of gene expression and tend to be localized at TAD boundaries, suggesting that these lincRNAs may influence chromosomal architecture. Keywords: intergenic long noncoding RNA, lincRNA, GWAS, expression quantitative trait loci, eQTL, complex trait and disease, enhancer, cis-regulation, topologically associated domains, TAD
Video coding and decoding devices and methods preserving ppg relevant information
2013-01-01
The present invention relates to a video encoding device (10) for encoding video data and a corresponding video decoding device, wherein during decoding PPG relevant information shall be preserved. For this purpose the video coding device (10) comprises a first encoder (20) for encoding input video
Structural imprints in vivo decode RNA regulatory mechanisms.
Spitale, Robert C; Flynn, Ryan A; Zhang, Qiangfeng Cliff; Crisalli, Pete; Lee, Byron; Jung, Jong-Wha; Kuchelmeister, Hannes Y; Batista, Pedro J; Torre, Eduardo A; Kool, Eric T; Chang, Howard Y
2015-03-26
Visualizing the physical basis for molecular behaviour inside living cells is a great challenge for biology. RNAs are central to biological regulation, and the ability of RNA to adopt specific structures intimately controls every step of the gene expression program. However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles include only two of the four nucleotides that make up RNA. Here we present a novel biochemical approach, in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE), which enables the first global view, to our knowledge, of RNA secondary structures in living cells for all four bases. icSHAPE of the mouse embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguish different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved from in vitro conditions, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA-binding proteins or RNA-modification sites that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N(6)-methyladenosine (m(6)A) modification genome wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.
Human Genome Research: Decoding DNA
dropdown arrow Site Map A-Z Index Menu Synopsis Human Genome Research: Decoding DNA Resources with of the DNA double helix during April 2003. James D. Watson, Francis Crick, and Maurice Wilkins were company Celera announced the completion of a "working draft" reference DNA sequence of the human
Decoder calibration with ultra small current sample set for intracortical brain-machine interface
Zhang, Peng; Ma, Xuan; Chen, Luyao; Zhou, Jin; Wang, Changyong; Li, Wei; He, Jiping
2018-04-01
Objective. Intracortical brain-machine interfaces (iBMIs) aim to restore efficient communication and movement ability for paralyzed patients. However, frequent recalibration is required for consistency and reliability, and every recalibration will require relatively large most current sample set. The aim in this study is to develop an effective decoder calibration method that can achieve good performance while minimizing recalibration time. Approach. Two rhesus macaques implanted with intracortical microelectrode arrays were trained separately on movement and sensory paradigm. Neural signals were recorded to decode reaching positions or grasping postures. A novel principal component analysis-based domain adaptation (PDA) method was proposed to recalibrate the decoder with only ultra small current sample set by taking advantage of large historical data, and the decoding performance was compared with other three calibration methods for evaluation. Main results. The PDA method closed the gap between historical and current data effectively, and made it possible to take advantage of large historical data for decoder recalibration in current data decoding. Using only ultra small current sample set (five trials of each category), the decoder calibrated using the PDA method could achieve much better and more robust performance in all sessions than using other three calibration methods in both monkeys. Significance. (1) By this study, transfer learning theory was brought into iBMIs decoder calibration for the first time. (2) Different from most transfer learning studies, the target data in this study were ultra small sample set and were transferred to the source data. (3) By taking advantage of historical data, the PDA method was demonstrated to be effective in reducing recalibration time for both movement paradigm and sensory paradigm, indicating a viable generalization. By reducing the demand for large current training data, this new method may facilitate the application
CERN. Geneva. Audiovisual Unit; Antonerakis, S E
2002-01-01
Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.
Discovery and development of new antibacterial drugs: learning from experience?
Jackson, Nicole; Czaplewski, Lloyd; Piddock, Laura J V
2018-06-01
Antibiotic (antibacterial) resistance is a serious global problem and the need for new treatments is urgent. The current antibiotic discovery model is not delivering new agents at a rate that is sufficient to combat present levels of antibiotic resistance. This has led to fears of the arrival of a 'post-antibiotic era'. Scientific difficulties, an unfavourable regulatory climate, multiple company mergers and the low financial returns associated with antibiotic drug development have led to the withdrawal of many pharmaceutical companies from the field. The regulatory climate has now begun to improve, but major scientific hurdles still impede the discovery and development of novel antibacterial agents. To facilitate discovery activities there must be increased understanding of the scientific problems experienced by pharmaceutical companies. This must be coupled with addressing the current antibiotic resistance crisis so that compounds and ultimately drugs are delivered to treat the most urgent clinical challenges. By understanding the causes of the failures and successes of the pharmaceutical industry's research history, duplication of discovery programmes will be reduced, increasing the productivity of the antibiotic drug discovery pipeline by academia and small companies. The most important scientific issues to address are getting molecules into the Gram-negative bacterial cell and avoiding their efflux. Hence screening programmes should focus their efforts on whole bacterial cells rather than cell-free systems. Despite falling out of favour with pharmaceutical companies, natural product research still holds promise for providing new molecules as a basis for discovery.
Biological 2-Input Decoder Circuit in Human Cells
2015-01-01
Decoders are combinational circuits that convert information from n inputs to a maximum of 2n outputs. This operation is of major importance in computing systems yet it is vastly underexplored in synthetic biology. Here, we present a synthetic gene network architecture that operates as a biological decoder in human cells, converting 2 inputs to 4 outputs. As a proof-of-principle, we use small molecules to emulate the two inputs and fluorescent reporters as the corresponding four outputs. The experiments are performed using transient transfections in human kidney embryonic cells and the characterization by fluorescence microscopy and flow cytometry. We show a clear separation between the ON and OFF mean fluorescent intensity states. Additionally, we adopt the integrated mean fluorescence intensity for the characterization of the circuit and show that this metric is more robust to transfection conditions when compared to the mean fluorescent intensity. To conclude, we present the first implementation of a genetic decoder. This combinational system can be valuable toward engineering higher-order circuits as well as accommodate a multiplexed interface with endogenous cellular functions. PMID:24694115
Biological 2-input decoder circuit in human cells.
Guinn, Michael; Bleris, Leonidas
2014-08-15
Decoders are combinational circuits that convert information from n inputs to a maximum of 2(n) outputs. This operation is of major importance in computing systems yet it is vastly underexplored in synthetic biology. Here, we present a synthetic gene network architecture that operates as a biological decoder in human cells, converting 2 inputs to 4 outputs. As a proof-of-principle, we use small molecules to emulate the two inputs and fluorescent reporters as the corresponding four outputs. The experiments are performed using transient transfections in human kidney embryonic cells and the characterization by fluorescence microscopy and flow cytometry. We show a clear separation between the ON and OFF mean fluorescent intensity states. Additionally, we adopt the integrated mean fluorescence intensity for the characterization of the circuit and show that this metric is more robust to transfection conditions when compared to the mean fluorescent intensity. To conclude, we present the first implementation of a genetic decoder. This combinational system can be valuable toward engineering higher-order circuits as well as accommodate a multiplexed interface with endogenous cellular functions.
Close Sequence Comparisons are Sufficient to Identify Humancis-Regulatory Elements
Energy Technology Data Exchange (ETDEWEB)
Prabhakar, Shyam; Poulin, Francis; Shoukry, Malak; Afzal, Veena; Rubin, Edward M.; Couronne, Olivier; Pennacchio, Len A.
2005-12-01
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of evolutionarily close and distant sequence comparisons, due to the lack of a universal metric for sequence conservation, and also the paucity of empirically defined benchmark sets of cis-regulatory elements. To address this problem, we developed a general-purpose algorithm (Gumby) that detects slowly-evolving regions in primate, mammalian and more distant comparisons without requiring adjustment of parameters, and ranks conserved elements by P-value using Karlin-Altschul statistics. We benchmarked Gumby predictions against previously identified cis-regulatory elements at diverse genomic loci, and also tested numerous extremely conserved human-rodent sequences for transcriptional enhancer activity using reporter-gene assays in transgenic mice. Human regulatory elements were identified with acceptable sensitivity and specificity by comparison with 1-5 other eutherian mammals or 6 other simian primates. More distant comparisons (marsupial, avian, amphibian and fish) failed to identify many of the empirically defined functional noncoding elements. We derived an intuitive relationship between ancient and recent noncoding sequence conservation from whole genome comparative analysis, which explains some of these findings. Lastly, we determined that, in addition to strength of conservation, genomic location and/or density of surrounding conserved elements must also be considered in selecting candidate enhancers for testing at embryonic time points.
How Major Depressive Disorder affects the ability to decode multimodal dynamic emotional stimuli
Directory of Open Access Journals (Sweden)
FILOMENA SCIBELLI
2016-09-01
Full Text Available Most studies investigating the processing of emotions in depressed patients reported impairments in the decoding of negative emotions. However, these studies adopted static stimuli (mostly stereotypical facial expressions corresponding to basic emotions which do not reflect the way people experience emotions in everyday life. For this reason, this work proposes to investigate the decoding of emotional expressions in patients affected by Recurrent Major Depressive Disorder (RMDDs using dynamic audio/video stimuli. RMDDs’ performance is compared with the performance of patients with Adjustment Disorder with Depressed Mood (ADs and healthy (HCs subjects. The experiments involve 27 RMDDs (16 with acute depression - RMDD-A, and 11 in a compensation phase - RMDD-C, 16 ADs and 16 HCs. The ability to decode emotional expressions is assessed through an emotion recognition task based on short audio (without video, video (without audio and audio/video clips. The results show that AD patients are significantly less accurate than HCs in decoding fear, anger, happiness, surprise and sadness. RMDD-As with acute depression are significantly less accurate than HCs in decoding happiness, sadness and surprise. Finally, no significant differences were found between HCs and RMDD-Cs in a compensation phase. The different communication channels and the types of emotion play a significant role in limiting the decoding accuracy.
Technical summaries of Scotian Shelf - significant and commercial discoveries
International Nuclear Information System (INIS)
Dickey, J.E.; Bigelow, S.F.; Edens, J.A.; Brown, D.E.; Smith, B.; Makrides, C.; Mader, R.
1997-03-01
An independent assessment of the recoverable hydrocarbon resource currently held under' Significant and Commercial Discovery' status offshore Nova Scotia was presented. A generalized description of the regulatory issues regarding the discovered resources within the Scotian Basin was included. Twenty discoveries have been declared significant and two have been declared commercial, pursuant to the Canada-Nova Scotia Offshore Petroleum Resources Accord Implementation Acts. Salient facts about each discovery were documented. The information included the wells drilled within the structure, significant flow tests, geological and geophysical attributes, structural cross-section and areal extent, petrophysical parameters, hydrocarbons in place and anticipated hydrocarbon recoverable resource. tabs., figs
A quantum algorithm for Viterbi decoding of classical convolutional codes
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.
Using Social Scientific Criteria to Evaluate Cultural Theories: Encoding/Decoding Evaluated
Directory of Open Access Journals (Sweden)
Evan L. Kropp
2015-12-01
Full Text Available This article transcends the issue of conflicting theoretical schools of thought to formulate a method of social scientific style theory evaluation for cultural studies. It is suggested that positivist social scientific models of theory critique can be used to assess cultural models of communication to determine if they should be classified as theories. A set of evaluation criteria is formulated as a guide and applied to Stuart Hall’s Encoding/Decoding to determine if it is a theory. Conclusions find the sharing of criteria between schools of thought is judicious, Encoding/Decoding fits the established criteria, and Encoding/Decoding should be referred to as a theory.
A Low-Complexity Joint Detection-Decoding Algorithm for Nonbinary LDPC-Coded Modulation Systems
Wang, Xuepeng; Bai, Baoming; Ma, Xiao
2010-01-01
In this paper, we present a low-complexity joint detection-decoding algorithm for nonbinary LDPC codedmodulation systems. The algorithm combines hard-decision decoding using the message-passing strategy with the signal detector in an iterative manner. It requires low computational complexity, offers good system performance and has a fast rate of decoding convergence. Compared to the q-ary sum-product algorithm (QSPA), it provides an attractive candidate for practical applications of q-ary LDP...
Neural Encoding and Decoding with Deep Learning for Dynamic Natural Vision.
Wen, Haiguang; Shi, Junxing; Zhang, Yizhen; Lu, Kun-Han; Cao, Jiayue; Liu, Zhongming
2017-10-20
Convolutional neural network (CNN) driven by image recognition has been shown to be able to explain cortical responses to static pictures at ventral-stream areas. Here, we further showed that such CNN could reliably predict and decode functional magnetic resonance imaging data from humans watching natural movies, despite its lack of any mechanism to account for temporal dynamics or feedback processing. Using separate data, encoding and decoding models were developed and evaluated for describing the bi-directional relationships between the CNN and the brain. Through the encoding models, the CNN-predicted areas covered not only the ventral stream, but also the dorsal stream, albeit to a lesser degree; single-voxel response was visualized as the specific pixel pattern that drove the response, revealing the distinct representation of individual cortical location; cortical activation was synthesized from natural images with high-throughput to map category representation, contrast, and selectivity. Through the decoding models, fMRI signals were directly decoded to estimate the feature representations in both visual and semantic spaces, for direct visual reconstruction and semantic categorization, respectively. These results corroborate, generalize, and extend previous findings, and highlight the value of using deep learning, as an all-in-one model of the visual cortex, to understand and decode natural vision. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Decoding sound level in the marmoset primary auditory cortex.
Sun, Wensheng; Marongelli, Ellisha N; Watkins, Paul V; Barbour, Dennis L
2017-10-01
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. NEW & NOTEWORTHY Neurons with nonmonotonic rate-level functions are unique to the central auditory system. These level-tuned neurons have been proposed to account for invariant sound perception across sound levels. Through systematic simulations based on real neuron responses, this study shows that neuron populations perform sound encoding optimally when containing both monotonic and nonmonotonic neurons. The results indicate that instead of working independently, nonmonotonic neurons complement the function of monotonic neurons in different sound-encoding contexts. Copyright © 2017 the American Physiological Society.
Jointly-check iterative decoding algorithm for quantum sparse graph codes
International Nuclear Information System (INIS)
Jun-Hu, Shao; Bao-Ming, Bai; Wei, Lin; Lin, Zhou
2010-01-01
For quantum sparse graph codes with stabilizer formalism, the unavoidable girth-four cycles in their Tanner graphs greatly degrade the iterative decoding performance with a standard belief-propagation (BP) algorithm. In this paper, we present a jointly-check iterative algorithm suitable for decoding quantum sparse graph codes efficiently. Numerical simulations show that this modified method outperforms the standard BP algorithm with an obvious performance improvement. (general)
High-Speed Soft-Decision Decoding of Two Reed-Muller Codes
Lin, Shu; Uehara, Gregory T.
1996-01-01
In his research, we have proposed the (64, 40, 8) subcode of the third-order Reed-Muller (RM) code to NASA for high-speed satellite communications. This RM subcode can be used either alone or as an inner code of a concatenated coding system with the NASA standard (255, 233, 33) Reed-Solomon (RS) code as the outer code to achieve high performance (or low bit-error rate) with reduced decoding complexity. It can also be used as a component code in a multilevel bandwidth efficient coded modulation system to achieve reliable bandwidth efficient data transmission. This report will summarize the key progress we have made toward achieving our eventual goal of implementing a decoder system based upon this code. In the first phase of study, we investigated the complexities of various sectionalized trellis diagrams for the proposed (64, 40, 8) RNI subcode. We found a specific 8-trellis diagram for this code which requires the least decoding complexity with a high possibility of achieving a decoding speed of 600 M bits per second (Mbps). The combination of a large number of states and a hi ch data rate will be made possible due to the utilization of a high degree of parallelism throughout the architecture. This trellis diagram will be presented and briefly described. In the second phase of study which was carried out through the past year, we investigated circuit architectures to determine the feasibility of VLSI implementation of a high-speed Viterbi decoder based on this 8-section trellis diagram. We began to examine specific design and implementation approaches to implement a fully custom integrated circuit (IC) which will be a key building block for a decoder system implementation. The key results will be presented in this report. This report will be divided into three primary sections. First, we will briefly describe the system block diagram in which the proposed decoder is assumed to be operating and present some of the key architectural approaches being used to
Efficient decoding of random errors for quantum expander codes
Fawzi , Omar; Grospellier , Antoine; Leverrier , Anthony
2017-01-01
We show that quantum expander codes, a constant-rate family of quantum LDPC codes, with the quasi-linear time decoding algorithm of Leverrier, Tillich and Z\\'emor can correct a constant fraction of random errors with very high probability. This is the first construction of a constant-rate quantum LDPC code with an efficient decoding algorithm that can correct a linear number of random errors with a negligible failure probability. Finding codes with these properties is also motivated by Gottes...
Multi-level trellis coded modulation and multi-stage decoding
Costello, Daniel J., Jr.; Wu, Jiantian; Lin, Shu
1990-01-01
Several constructions for multi-level trellis codes are presented and many codes with better performance than previously known codes are found. These codes provide a flexible trade-off between coding gain, decoding complexity, and decoding delay. New multi-level trellis coded modulation schemes using generalized set partitioning methods are developed for Quadrature Amplitude Modulation (QAM) and Phase Shift Keying (PSK) signal sets. New rotationally invariant multi-level trellis codes which can be combined with differential encoding to resolve phase ambiguity are presented.
Directory of Open Access Journals (Sweden)
Johann A. Briffa
2014-06-01
Full Text Available In this study, the authors consider time-varying block (TVB codes, which generalise a number of previous synchronisation error-correcting codes. They also consider various practical issues related to maximum a posteriori (MAP decoding of these codes. Specifically, they give an expression for the expected distribution of drift between transmitter and receiver because of synchronisation errors. They determine an appropriate choice for state space limits based on the drift probability distribution. In turn, they obtain an expression for the decoder complexity under given channel conditions in terms of the state space limits used. For a given state space, they also give a number of optimisations that reduce the algorithm complexity with no further loss of decoder performance. They also show how the MAP decoder can be used in the absence of known frame boundaries, and demonstrate that an appropriate choice of decoder parameters allows the decoder to approach the performance when frame boundaries are known, at the expense of some increase in complexity. Finally, they express some existing constructions as TVB codes, comparing performance with published results and showing that improved performance is possible by taking advantage of the flexibility of TVB codes.
Sequential decoders for large MIMO systems
Ali, Konpal S.; Abediseid, Walid; Alouini, Mohamed-Slim
2014-01-01
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
Deep learning with convolutional neural networks for EEG decoding and visualization.
Schirrmeister, Robin Tibor; Springenberg, Jost Tobias; Fiederer, Lukas Dominique Josef; Glasstetter, Martin; Eggensperger, Katharina; Tangermann, Michael; Hutter, Frank; Burgard, Wolfram; Ball, Tonio
2017-11-01
Deep learning with convolutional neural networks (deep ConvNets) has revolutionized computer vision through end-to-end learning, that is, learning from the raw data. There is increasing interest in using deep ConvNets for end-to-end EEG analysis, but a better understanding of how to design and train ConvNets for end-to-end EEG decoding and how to visualize the informative EEG features the ConvNets learn is still needed. Here, we studied deep ConvNets with a range of different architectures, designed for decoding imagined or executed tasks from raw EEG. Our results show that recent advances from the machine learning field, including batch normalization and exponential linear units, together with a cropped training strategy, boosted the deep ConvNets decoding performance, reaching at least as good performance as the widely used filter bank common spatial patterns (FBCSP) algorithm (mean decoding accuracies 82.1% FBCSP, 84.0% deep ConvNets). While FBCSP is designed to use spectral power modulations, the features used by ConvNets are not fixed a priori. Our novel methods for visualizing the learned features demonstrated that ConvNets indeed learned to use spectral power modulations in the alpha, beta, and high gamma frequencies, and proved useful for spatially mapping the learned features by revealing the topography of the causal contributions of features in different frequency bands to the decoding decision. Our study thus shows how to design and train ConvNets to decode task-related information from the raw EEG without handcrafted features and highlights the potential of deep ConvNets combined with advanced visualization techniques for EEG-based brain mapping. Hum Brain Mapp 38:5391-5420, 2017. © 2017 Wiley Periodicals, Inc. © 2017 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.
Deep learning with convolutional neural networks for EEG decoding and visualization
Springenberg, Jost Tobias; Fiederer, Lukas Dominique Josef; Glasstetter, Martin; Eggensperger, Katharina; Tangermann, Michael; Hutter, Frank; Burgard, Wolfram; Ball, Tonio
2017-01-01
Abstract Deep learning with convolutional neural networks (deep ConvNets) has revolutionized computer vision through end‐to‐end learning, that is, learning from the raw data. There is increasing interest in using deep ConvNets for end‐to‐end EEG analysis, but a better understanding of how to design and train ConvNets for end‐to‐end EEG decoding and how to visualize the informative EEG features the ConvNets learn is still needed. Here, we studied deep ConvNets with a range of different architectures, designed for decoding imagined or executed tasks from raw EEG. Our results show that recent advances from the machine learning field, including batch normalization and exponential linear units, together with a cropped training strategy, boosted the deep ConvNets decoding performance, reaching at least as good performance as the widely used filter bank common spatial patterns (FBCSP) algorithm (mean decoding accuracies 82.1% FBCSP, 84.0% deep ConvNets). While FBCSP is designed to use spectral power modulations, the features used by ConvNets are not fixed a priori. Our novel methods for visualizing the learned features demonstrated that ConvNets indeed learned to use spectral power modulations in the alpha, beta, and high gamma frequencies, and proved useful for spatially mapping the learned features by revealing the topography of the causal contributions of features in different frequency bands to the decoding decision. Our study thus shows how to design and train ConvNets to decode task‐related information from the raw EEG without handcrafted features and highlights the potential of deep ConvNets combined with advanced visualization techniques for EEG‐based brain mapping. Hum Brain Mapp 38:5391–5420, 2017. © 2017 Wiley Periodicals, Inc. PMID:28782865
Douik, Ahmed S.
2015-11-05
This paper considers the multicast decoding delay reduction problem for generalized instantly decodable network coding (G-IDNC) over persistent erasure channels with feedback imperfections. The feedback scenario discussed is the most general situation in which the sender does not always receive acknowledgments from the receivers after each transmission and the feedback communications are subject to loss. The decoding delay increment expressions are derived and employed to express the decoding delay reduction problem as a maximum weight clique problem in the G-IDNC graph. This paper provides a theoretical analysis of the expected decoding delay increase at each time instant. Problem formulations in simpler channel and feedback models are shown to be special cases of the proposed generalized formulation. Since finding the optimal solution to the problem is known to be NP-hard, a suboptimal greedy algorithm is designed and compared with blind approaches proposed in the literature. Through extensive simulations, the proposed algorithm is shown to outperform the blind methods in all situations and to achieve significant improvement, particularly for high time-correlated channels.
Analysis of error floor of LDPC codes under LP decoding over the BSC
Energy Technology Data Exchange (ETDEWEB)
Chertkov, Michael [Los Alamos National Laboratory; Chilappagari, Shashi [UNIV OF AZ; Vasic, Bane [UNIV OF AZ; Stepanov, Mikhail [UNIV OF AZ
2009-01-01
We consider linear programming (LP) decoding of a fixed low-density parity-check (LDPC) code over the binary symmetric channel (BSC). The LP decoder fails when it outputs a pseudo-codeword which is not a codeword. We propose an efficient algorithm termed the instanton search algorithm (ISA) which, given a random input, generates a set of flips called the BSC-instanton and prove that: (a) the LP decoder fails for any set of flips with support vector including an instanton; (b) for any input, the algorithm outputs an instanton in the number of steps upper-bounded by twice the number of flips in the input. We obtain the number of unique instantons of different sizes by running the ISA sufficient number of times. We then use the instanton statistics to predict the performance of the LP decoding over the BSC in the error floor region. We also propose an efficient semi-analytical method to predict the performance of LP decoding over a large range of transition probabilities of the BSC.
Douik, Ahmed S.; Sorour, Sameh; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim
2015-01-01
This paper considers the multicast decoding delay reduction problem for generalized instantly decodable network coding (G-IDNC) over persistent erasure channels with feedback imperfections. The feedback scenario discussed is the most general situation in which the sender does not always receive acknowledgments from the receivers after each transmission and the feedback communications are subject to loss. The decoding delay increment expressions are derived and employed to express the decoding delay reduction problem as a maximum weight clique problem in the G-IDNC graph. This paper provides a theoretical analysis of the expected decoding delay increase at each time instant. Problem formulations in simpler channel and feedback models are shown to be special cases of the proposed generalized formulation. Since finding the optimal solution to the problem is known to be NP-hard, a suboptimal greedy algorithm is designed and compared with blind approaches proposed in the literature. Through extensive simulations, the proposed algorithm is shown to outperform the blind methods in all situations and to achieve significant improvement, particularly for high time-correlated channels.
Horikawa, Tomoyasu; Kamitani, Yukiyasu
2017-01-01
Dreaming is generally thought to be generated by spontaneous brain activity during sleep with patterns common to waking experience. This view is supported by a recent study demonstrating that dreamed objects can be predicted from brain activity during sleep using statistical decoders trained with stimulus-induced brain activity. However, it remains unclear whether and how visual image features associated with dreamed objects are represented in the brain. In this study, we used a deep neural network (DNN) model for object recognition as a proxy for hierarchical visual feature representation, and DNN features for dreamed objects were analyzed with brain decoding of fMRI data collected during dreaming. The decoders were first trained with stimulus-induced brain activity labeled with the feature values of the stimulus image from multiple DNN layers. The decoders were then used to decode DNN features from the dream fMRI data, and the decoded features were compared with the averaged features of each object category calculated from a large-scale image database. We found that the feature values decoded from the dream fMRI data positively correlated with those associated with dreamed object categories at mid- to high-level DNN layers. Using the decoded features, the dreamed object category could be identified at above-chance levels by matching them to the averaged features for candidate categories. The results suggest that dreaming recruits hierarchical visual feature representations associated with objects, which may support phenomenal aspects of dream experience.
Distributed-phase OCDMA encoder-decoders based on fiber Bragg gratings
Zhang, Zhaowei; Tian, C.; Petropoulos, P.; Richardson, D.J.; Ibsen, M.
2007-01-01
We propose and demonstrate new optical code-division multiple-access (OCDMA) encoder-decoders having a continuous phase-distribution. With the same spatial refractive index distribution as the reconfigurable optical phase encoder-decoders, they are inherently suitable for the application in reconfigurable OCDMA systems. Furthermore, compared with conventional discrete-phase devices, they also have additional advantages of being more tolerant to input pulse width and, therefore, have the poten...
Long-Term Asynchronous Decoding of Arm Motion Using Electrocorticographic Signals in Monkeys
Chao, Zenas C.; Nagasaka, Yasuo; Fujii, Naotaka
2009-01-01
Brain–machine interfaces (BMIs) employ the electrical activity generated by cortical neurons directly for controlling external devices and have been conceived as a means for restoring human cognitive or sensory-motor functions. The dominant approach in BMI research has been to decode motor variables based on single-unit activity (SUA). Unfortunately, this approach suffers from poor long-term stability and daily recalibration is normally required to maintain reliable performance. A possible alternative is BMIs based on electrocorticograms (ECoGs), which measure population activity and may provide more durable and stable recording. However, the level of long-term stability that ECoG-based decoding can offer remains unclear. Here we propose a novel ECoG-based decoding paradigm and show that we have successfully decoded hand positions and arm joint angles during an asynchronous food-reaching task in monkeys when explicit cues prompting the onset of movement were not required. Performance using our ECoG-based decoder was comparable to existing SUA-based systems while evincing far superior stability and durability. In addition, the same decoder could be used for months without any drift in accuracy or recalibration. These results were achieved by incorporating the spatio-spectro-temporal integration of activity across multiple cortical areas to compensate for the lower fidelity of ECoG signals. These results show the feasibility of high-performance, chronic and versatile ECoG-based neuroprosthetic devices for real-life applications. This new method provides a stable platform for investigating cortical correlates for understanding motor control, sensory perception, and high-level cognitive processes. PMID:20407639
Neural decoding of visual imagery during sleep.
Horikawa, T; Tamaki, M; Miyawaki, Y; Kamitani, Y
2013-05-03
Visual imagery during sleep has long been a topic of persistent speculation, but its private nature has hampered objective analysis. Here we present a neural decoding approach in which machine-learning models predict the contents of visual imagery during the sleep-onset period, given measured brain activity, by discovering links between human functional magnetic resonance imaging patterns and verbal reports with the assistance of lexical and image databases. Decoding models trained on stimulus-induced brain activity in visual cortical areas showed accurate classification, detection, and identification of contents. Our findings demonstrate that specific visual experience during sleep is represented by brain activity patterns shared by stimulus perception, providing a means to uncover subjective contents of dreaming using objective neural measurement.
Linear-time general decoding algorithm for the surface code
Darmawan, Andrew S.; Poulin, David
2018-05-01
A quantum error correcting protocol can be substantially improved by taking into account features of the physical noise process. We present an efficient decoder for the surface code which can account for general noise features, including coherences and correlations. We demonstrate that the decoder significantly outperforms the conventional matching algorithm on a variety of noise models, including non-Pauli noise and spatially correlated noise. The algorithm is based on an approximate calculation of the logical channel using a tensor-network description of the noisy state.
Decoding visual object categories from temporal correlations of ECoG signals.
Majima, Kei; Matsuo, Takeshi; Kawasaki, Keisuke; Kawai, Kensuke; Saito, Nobuhito; Hasegawa, Isao; Kamitani, Yukiyasu
2014-04-15
How visual object categories are represented in the brain is one of the key questions in neuroscience. Studies on low-level visual features have shown that relative timings or phases of neural activity between multiple brain locations encode information. However, whether such temporal patterns of neural activity are used in the representation of visual objects is unknown. Here, we examined whether and how visual object categories could be predicted (or decoded) from temporal patterns of electrocorticographic (ECoG) signals from the temporal cortex in five patients with epilepsy. We used temporal correlations between electrodes as input features, and compared the decoding performance with features defined by spectral power and phase from individual electrodes. While using power or phase alone, the decoding accuracy was significantly better than chance, correlations alone or those combined with power outperformed other features. Decoding performance with correlations was degraded by shuffling the order of trials of the same category in each electrode, indicating that the relative time series between electrodes in each trial is critical. Analysis using a sliding time window revealed that decoding performance with correlations began to rise earlier than that with power. This earlier increase in performance was replicated by a model using phase differences to encode categories. These results suggest that activity patterns arising from interactions between multiple neuronal units carry additional information on visual object categories. Copyright © 2013 Elsevier Inc. All rights reserved.
An Optimized Three-Level Design of Decoder Based on Nanoscale Quantum-Dot Cellular Automata
Seyedi, Saeid; Navimipour, Nima Jafari
2018-03-01
Quantum-dot Cellular Automata (QCA) has been potentially considered as a supersede to Complementary Metal-Oxide-Semiconductor (CMOS) because of its inherent advantages. Many QCA-based logic circuits with smaller feature size, improved operating frequency, and lower power consumption than CMOS have been offered. This technology works based on electron relations inside quantum-dots. Due to the importance of designing an optimized decoder in any digital circuit, in this paper, we design, implement and simulate a new 2-to-4 decoder based on QCA with low delay, area, and complexity. The logic functionality of the 2-to-4 decoder is verified using the QCADesigner tool. The results have shown that the proposed QCA-based decoder has high performance in terms of a number of cells, covered area, and time delay. Due to the lower clock pulse frequency, the proposed 2-to-4 decoder is helpful for building QCA-based sequential digital circuits with high performance.
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.
Gao, Xin; Goggin, Kevin; Dowling, Camille; Qian, Jason; Hawdon, John M
2015-01-08
Hookworms infect nearly 700 million people, causing anemia and developmental stunting in heavy infections. Little is known about the genomic structure or gene regulation in hookworms, although recent publication of draft genome assemblies has allowed the first investigations of these topics to be undertaken. The transcription factor DAF-16 mediates multiple developmental pathways in the free living nematode Caenorhabditis elegans, and is involved in the recovery from the developmentally arrested L3 in hookworms. Identification of downstream targets of DAF-16 will provide a better understanding of the molecular mechanism of hookworm infection. Genomic Fragment 2.23 containing a DAF-16 binding element (DBE) was used to identify overlapping complementary expressed sequence tags (ESTs). These sequences were used to search a draft assembly of the Ancylostoma caninum genome, and identified two neighboring genes, snr-3 and lpp-1, in a tail-to-tail orientation. Expression patterns of both genes during parasitic development were determined by qRT-PCR. DAF-16 dependent cis-regulatory activity of fragment 2.23 was investigated using an in vitro reporter system. The snr-3 gene spans approximately 5.6 kb in the genome and contains 3 exons and 2 introns, and contains the DBE in its 3' untranslated region. Downstream from snr-3 in a tail-to-tail arrangement is the gene lpp-1. The lpp-1 gene spans more than 6 kb and contains 10 exons and 9 introns. The A. caninum genome contains 2 apparent splice variants, but there are 7 splice variants in the A. ceylanicum genome. While the gene order is similar, the gene structures of the hookworm genes differ from their C. elegans orthologs. Both genes show peak expression in the late L4 stage. Using a cell culture based expression system, fragment 2.23 was found to have both DAF-16-dependent promoter and enhancer activity that required an intact DBE. Two putative DAF-16 targets were identified by genome wide screening for DAF-16 binding
Identifying musical pieces from fMRI data using encoding and decoding models.
Hoefle, Sebastian; Engel, Annerose; Basilio, Rodrigo; Alluri, Vinoo; Toiviainen, Petri; Cagy, Maurício; Moll, Jorge
2018-02-02
Encoding models can reveal and decode neural representations in the visual and semantic domains. However, a thorough understanding of how distributed information in auditory cortices and temporal evolution of music contribute to model performance is still lacking in the musical domain. We measured fMRI responses during naturalistic music listening and constructed a two-stage approach that first mapped musical features in auditory cortices and then decoded novel musical pieces. We then probed the influence of stimuli duration (number of time points) and spatial extent (number of voxels) on decoding accuracy. Our approach revealed a linear increase in accuracy with duration and a point of optimal model performance for the spatial extent. We further showed that Shannon entropy is a driving factor, boosting accuracy up to 95% for music with highest information content. These findings provide key insights for future decoding and reconstruction algorithms and open new venues for possible clinical applications.
Gong, Wuming; Koyano-Nakagawa, Naoko; Li, Tongbin; Garry, Daniel J
2015-03-07
Decoding the temporal control of gene expression patterns is key to the understanding of the complex mechanisms that govern developmental decisions during heart development. High-throughput methods have been employed to systematically study the dynamic and coordinated nature of cardiac differentiation at the global level with multiple dimensions. Therefore, there is a pressing need to develop a systems approach to integrate these data from individual studies and infer the dynamic regulatory networks in an unbiased fashion. We developed a two-step strategy to integrate data from (1) temporal RNA-seq, (2) temporal histone modification ChIP-seq, (3) transcription factor (TF) ChIP-seq and (4) gene perturbation experiments to reconstruct the dynamic network during heart development. First, we trained a logistic regression model to predict the probability (LR score) of any base being bound by 543 TFs with known positional weight matrices. Second, four dimensions of data were combined using a time-varying dynamic Bayesian network model to infer the dynamic networks at four developmental stages in the mouse [mouse embryonic stem cells (ESCs), mesoderm (MES), cardiac progenitors (CP) and cardiomyocytes (CM)]. Our method not only infers the time-varying networks between different stages of heart development, but it also identifies the TF binding sites associated with promoter or enhancers of downstream genes. The LR scores of experimentally verified ESCs and heart enhancers were significantly higher than random regions (p network inference model identified a region with an elevated LR score approximately -9400 bp upstream of the transcriptional start site of Nkx2-5, which overlapped with a previously reported enhancer region (-9435 to -8922 bp). TFs such as Tead1, Gata4, Msx2, and Tgif1 were predicted to bind to this region and participate in the regulation of Nkx2-5 gene expression. Our model also predicted the key regulatory networks for the ESC-MES, MES-CP and CP
Stepwise encapsulation and controlled two-stage release system for cis-Diamminediiodoplatinum.
Chen, Yun; Li, Qian; Wu, Qingsheng
2014-01-01
cis-Diamminediiodoplatinum (cis-DIDP) is a cisplatin-like anticancer drug with higher anticancer activity, but lower stability and price than cisplatin. In this study, a cis-DIDP carrier system based on micro-sized stearic acid was prepared by an emulsion solvent evaporation method. The maximum drug loading capacity of cis-DIDP-loaded solid lipid nanoparticles was 22.03%, and their encapsulation efficiency was 97.24%. In vitro drug release in phosphate-buffered saline (pH =7.4) at 37.5°C exhibited a unique two-stage process, which could prove beneficial for patients with tumors and malignancies. MTT (3-[4,5-dimethylthiazol-2-yl]-2, 5-diphenyltetrazolium bromide) assay results showed that cis-DIDP released from cis-DIDP-loaded solid lipid nanoparticles had better inhibition activity than cis-DIDP that had not been loaded.
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...
A novel beat-noise-reducing en/decoding technology for a coherent 2-D OCDMA system.
Zheng, Jilin; Wang, Rong; Pu, Tao; Lu, Lin; Fang, Tao; Cheng, Yun; Chen, Xiangfei
2009-10-12
A novel fiber Bragg grating (FBG)-based en/decoder for a coherent two-dimensional (2-D) wavelength-time (WT) optical code-division multiple-access (OCDMA) system is proposed to suppress the beat noise (BN). The feasibility of en/decoding function and the effectiveness of BN suppression are demonstrated by the simulation comparison between the conventional and proposed scheme, which are also further validated by en/decoding experiments with two users at a data rate of 2.5, 5 and 10 Gb/s respectively. The further numerical performance analysis of the proposed en/decoding method reveals the BER improvement compared with the conventional system.
Yoles-Frenkel, Michal; Kahan, Anat; Ben-Shaul, Yoram
2018-05-23
The vomeronasal system (VNS) is a major vertebrate chemosensory system that functions in parallel to the main olfactory system (MOS). Despite many similarities, the two systems dramatically differ in the temporal domain. While MOS responses are governed by breathing and follow a subsecond temporal scale, VNS responses are uncoupled from breathing and evolve over seconds. This suggests that the contribution of response dynamics to stimulus information will differ between these systems. While temporal dynamics in the MOS are widely investigated, similar analyses in the accessory olfactory bulb (AOB) are lacking. Here, we have addressed this issue using controlled stimulus delivery to the vomeronasal organ of male and female mice. We first analyzed the temporal properties of AOB projection neurons and demonstrated that neurons display prolonged, variable, and neuron-specific characteristics. We then analyzed various decoding schemes using AOB population responses. We showed that compared with the simplest scheme (i.e., integration of spike counts over the entire response period), the division of this period into smaller temporal bins actually yields poorer decoding accuracy. However, optimal classification accuracy can be achieved well before the end of the response period by integrating spike counts within temporally defined windows. Since VNS stimulus uptake is variable, we analyzed decoding using limited information about stimulus uptake time, and showed that with enough neurons, such time-invariant decoding is feasible. Finally, we conducted simulations that demonstrated that, unlike the main olfactory bulb, the temporal features of AOB neurons disfavor decoding with high temporal accuracy, and, rather, support decoding without precise knowledge of stimulus uptake time. SIGNIFICANCE STATEMENT A key goal in sensory system research is to identify which metrics of neuronal activity are relevant for decoding stimulus features. Here, we describe the first systematic
Hardware Implementation of A Non-RLL Soft-decoding Beacon-based Visible Light Communication Receiver
Nguyen, Duc-Phuc; Le, Dinh-Dung; Tran, Thi-Hong; Huynh, Huu-Thuan; Nakashima, Yasuhiko
2018-01-01
Visible light communication (VLC)-based beacon systems, which usually transmit identification (ID) information in small-size data frames are applied widely in indoor localization applications. There is one fact that flicker of LED light should be avoid in any VLC systems. Current flicker mitigation solutions based on run-length limited (RLL) codes suffer from reduced code rates, or are limited to hard-decoding forward error correction (FEC) decoders. Recently, soft-decoding techniques of RLL-...
Relative Stability of cis- and trans-Hydrindanones
Directory of Open Access Journals (Sweden)
Motoo Tori
2015-01-01
Full Text Available The relative stabilities of several cis- and trans-hydrindanones were compared using both isomerization experiments and MM2 calculations. The generally believed rule that cis-hydrindanones are more stable than trans-isomers is applicable, but is not always true. This review introduces examples, mainly from studies in our laboratory, to explain these facts.
Mutiple LDPC Decoding using Bitplane Correlation for Transform Domain Wyner-Ziv Video Coding
DEFF Research Database (Denmark)
Luong, Huynh Van; Huang, Xin; Forchhammer, Søren
2011-01-01
Distributed video coding (DVC) is an emerging video coding paradigm for systems which fully or partly exploit the source statistics at the decoder to reduce the computational burden at the encoder. This paper considers a Low Density Parity Check (LDPC) based Transform Domain Wyner-Ziv (TDWZ) video...... codec. To improve the LDPC coding performance in the context of TDWZ, this paper proposes a Wyner-Ziv video codec using bitplane correlation through multiple parallel LDPC decoding. The proposed scheme utilizes inter bitplane correlation to enhance the bitplane decoding performance. Experimental results...
Decoding spikes in a spiking neuronal network
Energy Technology Data Exchange (ETDEWEB)
Feng Jianfeng [Department of Informatics, University of Sussex, Brighton BN1 9QH (United Kingdom); Ding, Mingzhou [Department of Mathematics, Florida Atlantic University, Boca Raton, FL 33431 (United States)
2004-06-04
We investigate how to reliably decode the input information from the output of a spiking neuronal network. A maximum likelihood estimator of the input signal, together with its Fisher information, is rigorously calculated. The advantage of the maximum likelihood estimation over the 'brute-force rate coding' estimate is clearly demonstrated. It is pointed out that the ergodic assumption in neuroscience, i.e. a temporal average is equivalent to an ensemble average, is in general not true. Averaging over an ensemble of neurons usually gives a biased estimate of the input information. A method on how to compensate for the bias is proposed. Reconstruction of dynamical input signals with a group of spiking neurons is extensively studied and our results show that less than a spike is sufficient to accurately decode dynamical inputs.
Decoding spikes in a spiking neuronal network
International Nuclear Information System (INIS)
Feng Jianfeng; Ding, Mingzhou
2004-01-01
We investigate how to reliably decode the input information from the output of a spiking neuronal network. A maximum likelihood estimator of the input signal, together with its Fisher information, is rigorously calculated. The advantage of the maximum likelihood estimation over the 'brute-force rate coding' estimate is clearly demonstrated. It is pointed out that the ergodic assumption in neuroscience, i.e. a temporal average is equivalent to an ensemble average, is in general not true. Averaging over an ensemble of neurons usually gives a biased estimate of the input information. A method on how to compensate for the bias is proposed. Reconstruction of dynamical input signals with a group of spiking neurons is extensively studied and our results show that less than a spike is sufficient to accurately decode dynamical inputs
2010-10-01
..., satellite, public switched telephone network, or any other source that uses the EAS protocol. (2) Valid..., analog radio and television broadcast stations, analog cable systems and wireless cable systems may... program data must be retained even with power removed. (7) Outputs. Decoders shall have the following...
Lexical decoder for continuous speech recognition: sequential neural network approach
International Nuclear Information System (INIS)
Iooss, Christine
1991-01-01
The work presented in this dissertation concerns the study of a connectionist architecture to treat sequential inputs. In this context, the model proposed by J.L. Elman, a recurrent multilayers network, is used. Its abilities and its limits are evaluated. Modifications are done in order to treat erroneous or noisy sequential inputs and to classify patterns. The application context of this study concerns the realisation of a lexical decoder for analytical multi-speakers continuous speech recognition. Lexical decoding is completed from lattices of phonemes which are obtained after an acoustic-phonetic decoding stage relying on a K Nearest Neighbors search technique. Test are done on sentences formed from a lexicon of 20 words. The results are obtained show the ability of the proposed connectionist model to take into account the sequentiality at the input level, to memorize the context and to treat noisy or erroneous inputs. (author) [fr
The Community Intercomparison Suite (CIS)
Watson-Parris, Duncan; Schutgens, Nick; Cook, Nick; Kipling, Zak; Kershaw, Phil; Gryspeerdt, Ed; Lawrence, Bryan; Stier, Philip
2017-04-01
Earth observations (both remote and in-situ) create vast amounts of data providing invaluable constraints for the climate science community. Efficient exploitation of these complex and highly heterogeneous datasets has been limited however by the lack of suitable software tools, particularly for comparison of gridded and ungridded data, thus reducing scientific productivity. CIS (http://cistools.net) is an open-source, command line tool and Python library which allows the straight-forward quantitative analysis, intercomparison and visualisation of remote sensing, in-situ and model data. The CIS can read gridded and ungridded remote sensing, in-situ and model data - and many other data sources 'out-of-the-box', such as ESA Aerosol and Cloud CCI product, MODIS, Cloud CCI, Cloudsat, AERONET. Perhaps most importantly however CIS also employs a modular plugin architecture to allow for the reading of limitless different data types. Users are able to write their own plugins for reading the data sources which they are familiar with, and share them within the community, allowing all to benefit from their expertise. To enable the intercomparison of this data the CIS provides a number of operations including: the aggregation of ungridded and gridded datasets to coarser representations using a number of different built in averaging kernels; the subsetting of data to reduce its extent or dimensionality; the co-location of two distinct datasets onto a single set of co-ordinates; the visualisation of the input or output data through a number of different plots and graphs; the evaluation of arbitrary mathematical expressions against any number of datasets; and a number of other supporting functions such as a statistical comparison of two co-located datasets. These operations can be performed efficiently on local machines or large computing clusters - and is already available on the JASMIN computing facility. A case-study using the GASSP collection of in-situ aerosol observations
A lossy graph model for delay reduction in generalized instantly decodable network coding
Douik, Ahmed S.; Sorour, Sameh; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim
2014-01-01
, arising from lossy feedback events, when the expected decoding delay of XORing them among themselves or with other certain packets is lower than that expected when sending these packets separately. We compare the decoding delay performance of LG-IDNC and G
An Area-Efficient Reconfigurable LDPC Decoder with Conflict Resolution
Zhou, Changsheng; Huang, Yuebin; Huang, Shuangqu; Chen, Yun; Zeng, Xiaoyang
Based on Turbo-Decoding Message-Passing (TDMP) and Normalized Min-Sum (NMS) algorithm, an area efficient LDPC decoder that supports both structured and unstructured LDPC codes is proposed in this paper. We introduce a solution to solve the memory access conflict problem caused by TDMP algorithm. We also arrange the main timing schedule carefully to handle the operations of our solution while avoiding much additional hardware consumption. To reduce the memory bits needed, the extrinsic message storing strategy is also optimized. Besides the extrinsic message recover and the accumulate operation are merged together. To verify our architecture, a LDPC decoder that supports both China Multimedia Mobile Broadcasting (CMMB) and Digital Terrestrial/ Television Multimedia Broadcasting (DTMB) standards is developed using SMIC 0.13µm standard CMOS process. The core area is 4.75mm2 and the maximum operating clock frequency is 200MHz. The estimated power consumption is 48.4mW at 25MHz for CMMB and 130.9mW at 50MHz for DTMB with 5 iterations and 1.2V supply.
Duuren, van, J.B.J.H.
2011-01-01
Optimization of Pseudomonas putida KT2440 as host for the production of cis, cis-muconate from benzoate P. putida KT2440 was used as biocatalyst given its versatile and energetically robust metabolism. Therefore, a mutant was generated and a process developed based on which a life cycle assessment (LCA) was performed. Additionally, the growth related parameters were experimentally obtained to constrain the metabolic model iJP815 further. The mutant Pseudomonas putida KT2440-JD1 was deri...
Cascading Oscillators in Decoding Speech: Reflection of a Cortical Computation Principle
2016-09-06
purely) auditory or articulatory model can explain this behavior. The insertion of gaps was interpreted as the act of providing extra decoding time...The windows are generated by a segmentation process, implemented by an array of cascaded oscillators. Correct segmentation is a critical...prerequisite for correct decoding, and segmentation is correct as long as the oscillators successfully track the input rhythms. Syllabic segmentation utilizes
Directory of Open Access Journals (Sweden)
Vito De Feo
2017-05-01
Full Text Available Brain-machine interfaces (BMIs promise to improve the quality of life of patients suffering from sensory and motor disabilities by creating a direct communication channel between the brain and the external world. Yet, their performance is currently limited by the relatively small amount of information that can be decoded from neural activity recorded form the brain. We have recently proposed that such decoding performance may be improved when using state-dependent decoding algorithms that predict and discount the large component of the trial-to-trial variability of neural activity which is due to the dependence of neural responses on the network's current internal state. Here we tested this idea by using a bidirectional BMI to investigate the gain in performance arising from using a state-dependent decoding algorithm. This BMI, implemented in anesthetized rats, controlled the movement of a dynamical system using neural activity decoded from motor cortex and fed back to the brain the dynamical system's position by electrically microstimulating somatosensory cortex. We found that using state-dependent algorithms that tracked the dynamics of ongoing activity led to an increase in the amount of information extracted form neural activity by 22%, with a consequently increase in all of the indices measuring the BMI's performance in controlling the dynamical system. This suggests that state-dependent decoding algorithms may be used to enhance BMIs at moderate computational cost.
De Feo, Vito; Boi, Fabio; Safaai, Houman; Onken, Arno; Panzeri, Stefano; Vato, Alessandro
2017-01-01
Brain-machine interfaces (BMIs) promise to improve the quality of life of patients suffering from sensory and motor disabilities by creating a direct communication channel between the brain and the external world. Yet, their performance is currently limited by the relatively small amount of information that can be decoded from neural activity recorded form the brain. We have recently proposed that such decoding performance may be improved when using state-dependent decoding algorithms that predict and discount the large component of the trial-to-trial variability of neural activity which is due to the dependence of neural responses on the network's current internal state. Here we tested this idea by using a bidirectional BMI to investigate the gain in performance arising from using a state-dependent decoding algorithm. This BMI, implemented in anesthetized rats, controlled the movement of a dynamical system using neural activity decoded from motor cortex and fed back to the brain the dynamical system's position by electrically microstimulating somatosensory cortex. We found that using state-dependent algorithms that tracked the dynamics of ongoing activity led to an increase in the amount of information extracted form neural activity by 22%, with a consequently increase in all of the indices measuring the BMI's performance in controlling the dynamical system. This suggests that state-dependent decoding algorithms may be used to enhance BMIs at moderate computational cost.
Joint Source-Channel Decoding of Variable-Length Codes with Soft Information: A Survey
Directory of Open Access Journals (Sweden)
Pierre Siohan
2005-05-01
Full Text Available Multimedia transmission over time-varying wireless channels presents a number of challenges beyond existing capabilities conceived so far for third-generation networks. Efficient quality-of-service (QoS provisioning for multimedia on these channels may in particular require a loosening and a rethinking of the layer separation principle. In that context, joint source-channel decoding (JSCD strategies have gained attention as viable alternatives to separate decoding of source and channel codes. A statistical framework based on hidden Markov models (HMM capturing dependencies between the source and channel coding components sets the foundation for optimal design of techniques of joint decoding of source and channel codes. The problem has been largely addressed in the research community, by considering both fixed-length codes (FLC and variable-length source codes (VLC widely used in compression standards. Joint source-channel decoding of VLC raises specific difficulties due to the fact that the segmentation of the received bitstream into source symbols is random. This paper makes a survey of recent theoretical and practical advances in the area of JSCD with soft information of VLC-encoded sources. It first describes the main paths followed for designing efficient estimators for VLC-encoded sources, the key component of the JSCD iterative structure. It then presents the main issues involved in the application of the turbo principle to JSCD of VLC-encoded sources as well as the main approaches to source-controlled channel decoding. This survey terminates by performance illustrations with real image and video decoding systems.
Joint Source-Channel Decoding of Variable-Length Codes with Soft Information: A Survey
Guillemot, Christine; Siohan, Pierre
2005-12-01
Multimedia transmission over time-varying wireless channels presents a number of challenges beyond existing capabilities conceived so far for third-generation networks. Efficient quality-of-service (QoS) provisioning for multimedia on these channels may in particular require a loosening and a rethinking of the layer separation principle. In that context, joint source-channel decoding (JSCD) strategies have gained attention as viable alternatives to separate decoding of source and channel codes. A statistical framework based on hidden Markov models (HMM) capturing dependencies between the source and channel coding components sets the foundation for optimal design of techniques of joint decoding of source and channel codes. The problem has been largely addressed in the research community, by considering both fixed-length codes (FLC) and variable-length source codes (VLC) widely used in compression standards. Joint source-channel decoding of VLC raises specific difficulties due to the fact that the segmentation of the received bitstream into source symbols is random. This paper makes a survey of recent theoretical and practical advances in the area of JSCD with soft information of VLC-encoded sources. It first describes the main paths followed for designing efficient estimators for VLC-encoded sources, the key component of the JSCD iterative structure. It then presents the main issues involved in the application of the turbo principle to JSCD of VLC-encoded sources as well as the main approaches to source-controlled channel decoding. This survey terminates by performance illustrations with real image and video decoding systems.
Abediseid, Walid
2012-12-21
The exact average complexity analysis of the basic sphere decoder for general space-time codes applied to multiple-input multiple-output (MIMO) wireless channel is known to be difficult. In this work, we shed the light on the computational complexity of sphere decoding for the quasi- static, lattice space-time (LAST) coded MIMO channel. Specifically, we drive an upper bound of the tail distribution of the decoder\\'s computational complexity. We show that when the computational complexity exceeds a certain limit, this upper bound becomes dominated by the outage probability achieved by LAST coding and sphere decoding schemes. We then calculate the minimum average computational complexity that is required by the decoder to achieve near optimal performance in terms of the system parameters. Our results indicate that there exists a cut-off rate (multiplexing gain) for which the average complexity remains bounded. Copyright © 2012 John Wiley & Sons, Ltd.
Delay reduction in persistent erasure channels for generalized instantly decodable network coding
Sorour, Sameh
2013-06-01
In this paper, we consider the problem of minimizing the decoding delay of generalized instantly decodable network coding (G-IDNC) in persistent erasure channels (PECs). By persistent erasure channels, we mean erasure channels with memory, which are modeled as a Gilbert-Elliott two-state Markov model with good and bad channel states. In this scenario, the channel erasure dependence, represented by the transition probabilities of this channel model, is an important factor that could be exploited to reduce the decoding delay. We first formulate the G-IDNC minimum decoding delay problem in PECs as a maximum weight clique problem over the G-IDNC graph. Since finding the optimal solution of this formulation is NP-hard, we propose two heuristic algorithms to solve it and compare them using extensive simulations. Simulation results show that each of these heuristics outperforms the other in certain ranges of channel memory levels. They also show that the proposed heuristics significantly outperform both the optimal strict IDNC in the literature and the channel-unaware G-IDNC algorithms. © 2013 IEEE.
Delay reduction in persistent erasure channels for generalized instantly decodable network coding
Sorour, Sameh; Aboutorab, Neda; Sadeghi, Parastoo; Karim, Mohammad Shahriar; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim
2013-01-01
In this paper, we consider the problem of minimizing the decoding delay of generalized instantly decodable network coding (G-IDNC) in persistent erasure channels (PECs). By persistent erasure channels, we mean erasure channels with memory, which are modeled as a Gilbert-Elliott two-state Markov model with good and bad channel states. In this scenario, the channel erasure dependence, represented by the transition probabilities of this channel model, is an important factor that could be exploited to reduce the decoding delay. We first formulate the G-IDNC minimum decoding delay problem in PECs as a maximum weight clique problem over the G-IDNC graph. Since finding the optimal solution of this formulation is NP-hard, we propose two heuristic algorithms to solve it and compare them using extensive simulations. Simulation results show that each of these heuristics outperforms the other in certain ranges of channel memory levels. They also show that the proposed heuristics significantly outperform both the optimal strict IDNC in the literature and the channel-unaware G-IDNC algorithms. © 2013 IEEE.
Gates, Louis
2017-12-11
The accompanying article introduces highly transparent grapheme-phoneme relationships embodied within a Periodic table of decoding cells, which arguably presents the quintessential transparent decoding elements. The study then folds these cells into one highly transparent but simply stated singularity generalization-this generalization unifies the decoding cells (97% transparency). Deeper, the periodic table and singularity generalization together highlight the connectivity of the periodic cells. Moreover, these interrelated cells, coupled with the singularity generalization, clarify teaching targets and enable efficient learning of the letter-sound code. This singularity generalization, in turn, serves as a model for creating unified but easily stated subordinate generalizations for any one of the transparent cells or groups of cells shown within the tables. The article then expands the periodic cells into two tables of teacher-ready sample word lists-one table includes sample words for the basic and phonogram vowel cells, and the other table embraces word samples for the transparent consonant cells. The paper concludes with suggestions for teaching the cellular transparency embedded within reoccurring isolated words and running text to promote decoding automaticity of the periodic cells.
Wimalaratne, Priyantha D C; Slessor, Keith N
2004-06-01
All four isomers of (Z)-3-cis-6,7-cis-9,10-diepoxyhenicosenes, 1-4, have been synthesized using D-xylose as the chirally pure starting material. D-Xylose was first converted to 2-deoxy-4,5-O-isopropylidene-3-t-butyldimethylsilyl-D-threopentose 11, via several steps of selective protection, dehydroxylation, and deprotection. Wittig coupling of 11 with nonyltriphenylphosphonium bromide followed by hydrogenation and acid catalyzed deprotection of hydroxyl groups yielded the chiral (2R,3R)-1,2,3-triol, 14, which was used as the precursor for the C-8 to C-21 unit of the (Z)-3-cis-6,7-cis-9,10-diepoxyhenicosenes. Selective tosylation of 14 followed by stereospecific cyclization yielded (2R,3R)-1,2-epoxytetradecan-3-ol, 16, which was then divergently converted to the t-butyldimethylsilyl ether 17 and tosylate 22, respectively. Establishment of the C-5 through C-7 unit of the target molecules was accomplished via regiospecific coupling of 17 with 1-t-butyldimethylsiloxy-2-propyne to form 18. Stepwise transformation of 18 via the formation of tosylate 19, desilylation, and stereospecific cyclization to form epoxy alcohol 20, followed by P2-Ni reduction yielded a key intermediate, allylic epoxy alcohol (Z)-2-(5S,6R)-cis-5,6-epoxyheptadecen-1-ol, 21. Similarly, the coupling of 22 with 1-t-butyldimethylsiloxy-2-propyne yielded 23, which was stereospecifically cyclized to form 24. Desilylation and P2-Ni reduction of 24 gave the antipodal intermediate, (Z)-2-(5R,6S)-cis-5,6-epoxyheptadecen-1-ol, 26. Asymmetric epoxidation of antipodes 21 and 26 with (L)- or (D)-diethyl tartrates resulted in the formation of diepoxy alcohols 27 and 29 from 21, and 33 and 31 from 26, respectively. Tosylation of these diepoxy alcohols followed by coupling with lithium dibutenyl cuprate yielded the four stereoisomers of (Z)-3-cis-6,7-cis-9,10-diepoxyhenicosenes, 1-4. Analysis of the retention characteristics of these materials revealed that one or both of the S*,R*,S*,R* stereoisomers comprise the
Model-driven discovery of underground metabolic functions in Escherichia coli
DEFF Research Database (Denmark)
Guzmán, Gabriela I.; Utrilla, José; Nurk, Sergey
2015-01-01
-scale models, which have been widely used for predicting growth phenotypes in various environments or following a genetic perturbation; however, these predictions occasionally fail. Failed predictions of gene essentiality offer an opportunity for targeting biological discovery, suggesting the presence......E, and gltA and prpC. This study demonstrates how a targeted model-driven approach to discovery can systematically fill knowledge gaps, characterize underground metabolism, and elucidate regulatory mechanisms of adaptation in response to gene KO perturbations....
The Contribution of Attentional Control and Working Memory to Reading Comprehension and Decoding
Arrington, C. Nikki; Kulesz, Paulina A.; Francis, David J.; Fletcher, Jack M.; Barnes, Marcia A.
2014-01-01
Little is known about how specific components of working memory, namely, attentional processes including response inhibition, sustained attention, and cognitive inhibition, are related to reading decoding and comprehension. The current study evaluated the relations of reading comprehension, decoding, working memory, and attentional control in…
Directory of Open Access Journals (Sweden)
Kang Keunsoo
2013-01-01
Full Text Available Abstract Background Cytokine-activated transcription factors from the STAT (Signal Transducers and Activators of Transcription family control common and context-specific genetic programs. It is not clear to what extent cell-specific features determine the binding capacity of seven STAT members and to what degree they share genetic targets. Molecular insight into the biology of STATs was gained from a meta-analysis of 29 available ChIP-seq data sets covering genome-wide occupancy of STATs 1, 3, 4, 5A, 5B and 6 in several cell types. Results We determined that the genomic binding capacity of STATs is primarily defined by the cell type and to a lesser extent by individual family members. For example, the overlap of shared binding sites between STATs 3 and 5 in T cells is greater than that between STAT5 in T cells and non-T cells. Even for the top 1,000 highly enriched STAT binding sites, ~15% of STAT5 binding sites in mouse female liver are shared by other STATs in different cell types while in T cells ~90% of STAT5 binding sites are co-occupied by STAT3, STAT4 and STAT6. In addition, we identified 116 cis-regulatory modules (CRM, which are recognized by all STAT members across cell types defining a common JAK-STAT signature. Lastly, in liver STAT5 binding significantly coincides with binding of the cell-specific transcription factors HNF4A, FOXA1 and FOXA2 and is associated with cell-type specific gene transcription. Conclusions Our results suggest that genomic binding of STATs is primarily determined by the cell type and further specificity is achieved in part by juxtaposed binding of cell-specific transcription factors.
Czech Academy of Sciences Publication Activity Database
Duraisamy, Ganesh Selvaraj; Mishra, Ajay Kumar; Kocábek, Tomáš; Matoušek, Jaroslav
2016-01-01
Roč. 84, October (2016), s. 346-352 ISSN 1476-9271 R&D Projects: GA ČR GA13-03037S Institutional support: RVO:60077344 Keywords : Cis-acting elements * Gene regulation * Humulus lupulus Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.331, year: 2016
Electronic Data Discovery: Integrating Due Process into Cyber Forensic Practice
Directory of Open Access Journals (Sweden)
John W. Bagby
2006-03-01
Full Text Available Most organizations and government agencies regularly become engaged in litigation with suppliers, customers, clients, employees, competitors, shareholders, prosecutors or regulatory agencies that nearly assures the need to organize, retain, find and produce business records and correspondence, e-mails, accounting records or other data relevant to disputed issues. This article discusses some high visibility cases that constrain how metadata and content is routinely made available to opposing parties in civil litigation, to prosecutors in criminal prosecutions and to agency staff in regulatory enforcement litigation. Public policy, as implemented in the rules of evidence and pretrial discovery, restrict electronic data discovery (EDD as it becomes a predominant and potentially costly pre-trial activity pivotal to modern litigation. This article discusses these constraints while identifying opportunities for the interdisciplinary activities among litigators, forensic experts and information technology professionals.
"ON ALGEBRAIC DECODING OF Q-ARY REED-MULLER AND PRODUCT REED-SOLOMON CODES"
Energy Technology Data Exchange (ETDEWEB)
SANTHI, NANDAKISHORE [Los Alamos National Laboratory
2007-01-22
We consider a list decoding algorithm recently proposed by Pellikaan-Wu for q-ary Reed-Muller codes RM{sub q}({ell}, m, n) of length n {le} q{sup m} when {ell} {le} q. A simple and easily accessible correctness proof is given which shows that this algorithm achieves a relative error-correction radius of {tau} {le} (1-{radical}{ell}q{sup m-1}/n). This is an improvement over the proof using one-point Algebraic-Geometric decoding method given in. The described algorithm can be adapted to decode product Reed-Solomon codes. We then propose a new low complexity recursive aJgebraic decoding algorithm for product Reed-Solomon codes and Reed-Muller codes. This algorithm achieves a relative error correction radius of {tau} {le} {Pi}{sub i=1}{sup m} (1 - {radical}k{sub i}/q). This algorithm is then proved to outperform the Pellikaan-Wu algorithm in both complexity and error correction radius over a wide range of code rates.
Population coding and decoding in a neural field: a computational study.
Wu, Si; Amari, Shun-Ichi; Nakahara, Hiroyuki
2002-05-01
This study uses a neural field model to investigate computational aspects of population coding and decoding when the stimulus is a single variable. A general prototype model for the encoding process is proposed, in which neural responses are correlated, with strength specified by a gaussian function of their difference in preferred stimuli. Based on the model, we study the effect of correlation on the Fisher information, compare the performances of three decoding methods that differ in the amount of encoding information being used, and investigate the implementation of the three methods by using a recurrent network. This study not only rediscovers main results in existing literatures in a unified way, but also reveals important new features, especially when the neural correlation is strong. As the neural correlation of firing becomes larger, the Fisher information decreases drastically. We confirm that as the width of correlation increases, the Fisher information saturates and no longer increases in proportion to the number of neurons. However, we prove that as the width increases further--wider than (sqrt)2 times the effective width of the turning function--the Fisher information increases again, and it increases without limit in proportion to the number of neurons. Furthermore, we clarify the asymptotic efficiency of the maximum likelihood inference (MLI) type of decoding methods for correlated neural signals. It shows that when the correlation covers a nonlocal range of population (excepting the uniform correlation and when the noise is extremely small), the MLI type of method, whose decoding error satisfies the Cauchy-type distribution, is not asymptotically efficient. This implies that the variance is no longer adequate to measure decoding accuracy.
Decoding facial expressions based on face-selective and motion-sensitive areas.
Liang, Yin; Liu, Baolin; Xu, Junhai; Zhang, Gaoyan; Li, Xianglin; Wang, Peiyuan; Wang, Bin
2017-06-01
Humans can easily recognize others' facial expressions. Among the brain substrates that enable this ability, considerable attention has been paid to face-selective areas; in contrast, whether motion-sensitive areas, which clearly exhibit sensitivity to facial movements, are involved in facial expression recognition remained unclear. The present functional magnetic resonance imaging (fMRI) study used multi-voxel pattern analysis (MVPA) to explore facial expression decoding in both face-selective and motion-sensitive areas. In a block design experiment, participants viewed facial expressions of six basic emotions (anger, disgust, fear, joy, sadness, and surprise) in images, videos, and eyes-obscured videos. Due to the use of multiple stimulus types, the impacts of facial motion and eye-related information on facial expression decoding were also examined. It was found that motion-sensitive areas showed significant responses to emotional expressions and that dynamic expressions could be successfully decoded in both face-selective and motion-sensitive areas. Compared with static stimuli, dynamic expressions elicited consistently higher neural responses and decoding performance in all regions. A significant decrease in both activation and decoding accuracy due to the absence of eye-related information was also observed. Overall, the findings showed that emotional expressions are represented in motion-sensitive areas in addition to conventional face-selective areas, suggesting that motion-sensitive regions may also effectively contribute to facial expression recognition. The results also suggested that facial motion and eye-related information played important roles by carrying considerable expression information that could facilitate facial expression recognition. Hum Brain Mapp 38:3113-3125, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers
Directory of Open Access Journals (Sweden)
Kuzin Alexander
2008-08-01
Full Text Available Abstract Background The presence of highly conserved sequences within cis-regulatory regions can serve as a valuable starting point for elucidating the basis of enhancer function. This study focuses on regulation of gene expression during the early events of Drosophila neural development. We describe the use of EvoPrinter and cis-Decoder, a suite of interrelated phylogenetic footprinting and alignment programs, to characterize highly conserved sequences that are shared among co-regulating enhancers. Results Analysis of in vivo characterized enhancers that drive neural precursor gene expression has revealed that they contain clusters of highly conserved sequence blocks (CSBs made up of shorter shared sequence elements which are present in different combinations and orientations within the different co-regulating enhancers; these elements contain either known consensus transcription factor binding sites or consist of novel sequences that have not been functionally characterized. The CSBs of co-regulated enhancers share a large number of sequence elements, suggesting that a diverse repertoire of transcription factors may interact in a highly combinatorial fashion to coordinately regulate gene expression. We have used information gained from our comparative analysis to discover an enhancer that directs expression of the nervy gene in neural precursor cells of the CNS and PNS. Conclusion The combined use EvoPrinter and cis-Decoder has yielded important insights into the combinatorial appearance of fundamental sequence elements required for neural enhancer function. Each of the 30 enhancers examined conformed to a pattern of highly conserved blocks of sequences containing shared constituent elements. These data establish a basis for further analysis and understanding of neural enhancer function.
Decoding Pigeon Behavior Outcomes Using Functional Connections among Local Field Potentials.
Chen, Yan; Liu, Xinyu; Li, Shan; Wan, Hong
2018-01-01
Recent studies indicate that the local field potential (LFP) carries information about an animal's behavior, but issues regarding whether there are any relationships between the LFP functional networks and behavior tasks as well as whether it is possible to employ LFP network features to decode the behavioral outcome in a single trial remain unresolved. In this study, we developed a network-based method to decode the behavioral outcomes in pigeons by using the functional connectivity strength values among LFPs recorded from the nidopallium caudolaterale (NCL). In our method, the functional connectivity strengths were first computed based on the synchronization likelihood. Second, the strength values were unwrapped into row vectors and their dimensions were then reduced by principal component analysis. Finally, the behavioral outcomes in single trials were decoded using leave-one-out combined with the k -nearest neighbor method. The results showed that the LFP functional network based on the gamma-band was related to the goal-directed behavior of pigeons. Moreover, the accuracy of the network features (74 ± 8%) was significantly higher than that of the power features (61 ± 12%). The proposed method provides a powerful tool for decoding animal behavior outcomes using a neural functional network.
Roundup litigation discovery documents: implications for public health and journal ethics.
Krimsky, Sheldon; Gillam, Carey
2018-06-08
This paper reviews the court-released discovery documents obtained from litigation against Monsanto over its herbicide Roundup and through Freedom of Information Act requests (requests to regulatory agencies and public universities in the United States). We sought evidence of corporate malfeasance and undisclosed conflicts of interest with respect to issues of scientific integrity. The findings include evidence of ghostwriting, interference in journal publication, and undue influence of a federal regulatory agency.
CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites.
Sharpe, Richard M; Koepke, Tyson; Harper, Artemus; Grimes, John; Galli, Marco; Satoh-Cruz, Mio; Kalyanaraman, Ananth; Evans, Katherine; Kramer, David; Dhingra, Amit
2016-01-01
High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. CisSERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. CisSERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, CisSERS utilizes the REBASE enzyme database. Results from CisSERS enable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3'UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. CisSERS is a java based graphical user interface built around a perl backbone. Several of the applications of CisSERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool CisSERS and results from in-silico and corresponding wet-lab analyses demonstrating that CisSERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.
Monoclonal antibodies to DNA modified with cis- or trans-diamminedichloroplatinum(II)
International Nuclear Information System (INIS)
Sundquist, W.I.; Lippard, S.J.; Stollar, B.D.
1987-01-01
Murine monoclonal antibodies that bind selectively to adducts formed on DNA by the antitumor drug cis-diamminedichloroplatinum(II), cis-DDP, or to the chemothrapeutically inactive trans isomer trans-DDP were elicited by immunization with calf thymus DNA modified with either cis- or trans-DDP at ratios of bound platinum per nucleotide, (D/N)/sub b/, of 0.06-0.08. The binding of two monoclonal antibodies to cis-DDP-modified DNA was competitively inhibited in an enzyme-linked immunosorbent assay (ELISA) by 4-6 nM concentrations of cis-DDP bound to DNA. Adducts formed by cis-DDP on other synthetic DNA polymers did not inhibit antibody binding to cis-DDP-DNA. The biologically active compounds [Pt(en)Cl 2 ], [Pt(dach)Cl 2 ], and [Pt(NH 3 ) 2 (cbdca)] (carboplatin) all formed antibody-detectable adducts on DNA, whereas the inactive platinum complexes trans-DDP and [Pt(dien)Cl]Cl (dien, diethylenetriamine) did not. The monoclonal antibodies therefore recognize a bifunctional Pt-DNA adduct with cis stereochemistry in which platinum is coordinated by two adjacent guanines or, to a lesser degree, by adjacent adenine and guanine. A monoclonal antibody raised against trans-DDP-DNA was competitively inhibited in an ELISA by 40 nM trans-DDP bound to DNA. This antibody crossreacted with unmodified, denatured DNA. The recognition of cis- or trans-DDP-modified DNAs by monoclonal antibodies thus parallels the known modes of DNA binding of these compounds and may correlate with their biological activities
Stepwise encapsulation and controlled two-stage release system for cis-Diamminediiodoplatinum
Directory of Open Access Journals (Sweden)
Chen Y
2014-06-01
Full Text Available Yun Chen,1,* Qian Li,1,2,* Qingsheng Wu1 1Department of Chemistry, Key Laboratory of Yangtze River Water Environment, Ministry of Education, Tongji University, Shanghai; 2Shanghai Institute of Quality Inspection and Technical Research, Shanghai, People’s Republic of China *These authors contributed equally to this work Abstract: cis-Diamminediiodoplatinum (cis-DIDP is a cisplatin-like anticancer drug with higher anticancer activity, but lower stability and price than cisplatin. In this study, a cis-DIDP carrier system based on micro-sized stearic acid was prepared by an emulsion solvent evaporation method. The maximum drug loading capacity of cis-DIDP-loaded solid lipid nanoparticles was 22.03%, and their encapsulation efficiency was 97.24%. In vitro drug release in phosphate-buffered saline (pH =7.4 at 37.5°C exhibited a unique two-stage process, which could prove beneficial for patients with tumors and malignancies. MTT (3-[4,5-dimethylthiazol-2-yl]-2, 5-diphenyltetrazolium bromide assay results showed that cis-DIDP released from cis-DIDP-loaded solid lipid nanoparticles had better inhibition activity than cis-DIDP that had not been loaded. Keywords: stearic acid, emulsion solvent evaporation method, drug delivery, cis-DIDP, in vitro
Connections between Transcription Downstream of Genes and cis-SAGe Chimeric RNA.
Chwalenia, Katarzyna; Qin, Fujun; Singh, Sandeep; Tangtrongstittikul, Panjapon; Li, Hui
2017-11-22
cis-Splicing between adjacent genes (cis-SAGe) is being recognized as one way to produce chimeric fusion RNAs. However, its detail mechanism is not clear. Recent study revealed induction of transcriptions downstream of genes (DoGs) under osmotic stress. Here, we investigated the influence of osmotic stress on cis-SAGe chimeric RNAs and their connection to DoGs. We found,the absence of induction of at least some cis-SAGe fusions and/or their corresponding DoGs at early time point(s). In fact, these DoGs and their cis-SAGe fusions are inversely correlated. This negative correlation was changed to positive at a later time point. These results suggest a direct competition between the two categories of transcripts when total pool of readthrough transcripts is limited at an early time point. At a later time point, DoGs and corresponding cis-SAGe fusions are both induced, indicating that total readthrough transcripts become more abundant. Finally, we observed overall enhancement of cis-SAGe chimeric RNAs in KCl-treated samples by RNA-Seq analysis.
Enantioselective disruption of the endocrine system by Cis-Bifenthrin in the male mice.
Jin, Yuanxiang; Wang, Jiangcong; Pan, Xiuhong; Miao, Wenyu; Lin, Xiaojian; Wang, Linggang; Fu, Zhengwei
2015-07-01
Bifenthrin (BF), as a chiral pyrethroid, is widely used to control field and household pests in China. At present, the commercial BF is a mixed compound containing cis isomers (cis-BF) including two enantiomers of 1R-cis-BF and 1S-cis-BF. In the present study, the two individual cis-BF enantiomers were separated by a preparative supercritical fluid chromatography. Then, four week-old adolescent male ICR mice were orally administered 1R-cis-BF and 1S-cis-BF separately daily for 3 weeks at doses of 0, 7.5 and 15 mg/kg/day, respectively. Results showed that the transcription status of some genes involved in cholesterol synthesis and transport as well as testosterone (T) synthesis in the testes were influenced by cis-BF enantiomers. Especially, we observed that the transcription status of key genes on the pathway of T synthesis including cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc) and cytochrome P450 17α-hydroxysteroid dehydrogenase (P45017α)) were selectively altered in the testis of mice when treated with 1S-cis-BF, suggesting that it is the possible reason to explain why the lower serum T concentration in 1S-cis-BF treated group. Taken together, it concluded that both of the cis-BF enantiomers have the endocrine disruption activities, while 1S-cis-BF was higher than 1R-cis-BF in mice when exposed during the puberty. The data was helpful to understand the toxicity of cis-BF in mammals under enantiomeric level. © 2014 Wiley Periodicals, Inc.
Logical knowledge representation of regulatory relations in biomedical pathways
DEFF Research Database (Denmark)
Zambach, Sine; Hansen, Jens Ulrik
2010-01-01
Knowledge on regulatory relations, in for example regulatory pathways in biology, is used widely in experiment design by biomedical researchers and in systems biology. The knowledge has typically either been represented through simple graphs or through very expressive differential equation...... simulations of smaller parts of a pathway. In this work we suggest a knowledge representation of the most basic relations in regulatory processes regulates, positively regulates and negatively regulates in logics based on a semantic analysis. We discuss the usage of these relations in biology and in articial...... intelligence for hypothesis development in drug discovery....
Du, Jing; Wang, Jian
2015-11-01
Bessel beams carrying orbital angular momentum (OAM) with helical phase fronts exp(ilφ)(l=0;±1;±2;…), where φ is the azimuthal angle and l corresponds to the topological number, are orthogonal with each other. This feature of Bessel beams provides a new dimension to code/decode data information on the OAM state of light, and the theoretical infinity of topological number enables possible high-dimensional structured light coding/decoding for free-space optical communications. Moreover, Bessel beams are nondiffracting beams having the ability to recover by themselves in the face of obstructions, which is important for free-space optical communications relying on line-of-sight operation. By utilizing the OAM and nondiffracting characteristics of Bessel beams, we experimentally demonstrate 12 m distance obstruction-free optical m-ary coding/decoding using visible Bessel beams in a free-space optical communication system. We also study the bit error rate (BER) performance of hexadecimal and 32-ary coding/decoding based on Bessel beams with different topological numbers. After receiving 500 symbols at the receiver side, a zero BER of hexadecimal coding/decoding is observed when the obstruction is placed along the propagation path of light.
Genome-wide discovery of drug-dependent human liver regulatory elements.
Directory of Open Access Journals (Sweden)
Robin P Smith
2014-10-01
Full Text Available Inter-individual variation in gene regulatory elements is hypothesized to play a causative role in adverse drug reactions and reduced drug activity. However, relatively little is known about the location and function of drug-dependent elements. To uncover drug-associated elements in a genome-wide manner, we performed RNA-seq and ChIP-seq using antibodies against the pregnane X receptor (PXR and three active regulatory marks (p300, H3K4me1, H3K27ac on primary human hepatocytes treated with rifampin or vehicle control. Rifampin and PXR were chosen since they are part of the CYP3A4 pathway, which is known to account for the metabolism of more than 50% of all prescribed drugs. We selected 227 proximal promoters for genes with rifampin-dependent expression or nearby PXR/p300 occupancy sites and assayed their ability to induce luciferase in rifampin-treated HepG2 cells, finding only 10 (4.4% that exhibited drug-dependent activity. As this result suggested a role for distal enhancer modules, we searched more broadly to identify 1,297 genomic regions bearing a conditional PXR occupancy as well as all three active regulatory marks. These regions are enriched near genes that function in the metabolism of xenobiotics, specifically members of the cytochrome P450 family. We performed enhancer assays in rifampin-treated HepG2 cells for 42 of these sequences as well as 7 sequences that overlap linkage-disequilibrium blocks defined by lead SNPs from pharmacogenomic GWAS studies, revealing 15/42 and 4/7 to be functional enhancers, respectively. A common African haplotype in one of these enhancers in the GSTA locus was found to exhibit potential rifampin hypersensitivity. Combined, our results further suggest that enhancers are the predominant targets of rifampin-induced PXR activation, provide a genome-wide catalog of PXR targets and serve as a model for the identification of drug-responsive regulatory elements.
Decoding Speech With Integrated Hybrid Signals Recorded From the Human Ventral Motor Cortex
Directory of Open Access Journals (Sweden)
Kenji Ibayashi
2018-04-01
Full Text Available Restoration of speech communication for locked-in patients by means of brain computer interfaces (BCIs is currently an important area of active research. Among the neural signals obtained from intracranial recordings, single/multi-unit activity (SUA/MUA, local field potential (LFP, and electrocorticography (ECoG are good candidates for an input signal for BCIs. However, the question of which signal or which combination of the three signal modalities is best suited for decoding speech production remains unverified. In order to record SUA, LFP, and ECoG simultaneously from a highly localized area of human ventral sensorimotor cortex (vSMC, we fabricated an electrode the size of which was 7 by 13 mm containing sparsely arranged microneedle and conventional macro contacts. We determined which signal modality is the most capable of decoding speech production, and tested if the combination of these signals could improve the decoding accuracy of spoken phonemes. Feature vectors were constructed from spike frequency obtained from SUAs and event-related spectral perturbation derived from ECoG and LFP signals, then input to the decoder. The results showed that the decoding accuracy for five spoken vowels was highest when features from multiple signals were combined and optimized for each subject, and reached 59% when averaged across all six subjects. This result suggests that multi-scale signals convey complementary information for speech articulation. The current study demonstrated that simultaneous recording of multi-scale neuronal activities could raise decoding accuracy even though the recording area is limited to a small portion of cortex, which is advantageous for future implementation of speech-assisting BCIs.
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.
Performance Analysis of Iterative Decoding Algorithms for PEG LDPC Codes in Nakagami Fading Channels
Directory of Open Access Journals (Sweden)
O. Al Rasheed
2013-11-01
Full Text Available In this paper we give a comparative analysis of decoding algorithms of Low Density Parity Check (LDPC codes in a channel with the Nakagami distribution of the fading envelope. We consider the Progressive Edge-Growth (PEG method and Improved PEG method for the parity check matrix construction, which can be used to avoid short girths, small trapping sets and a high level of error floor. A comparative analysis of several classes of LDPC codes in various propagation conditions and decoded using different decoding algorithms is also presented.
Directory of Open Access Journals (Sweden)
David Perez-Diaz de Cerio
2017-03-01
Full Text Available The purpose of this paper is to evaluate from a real perspective the performance of Bluetooth Low Energy (BLE as a technology that enables fast and reliable discovery of a large number of users/devices in a short period of time. The BLE standard specifies a wide range of configurable parameter values that determine the discovery process and need to be set according to the particular application requirements. Many previous works have been addressed to investigate the discovery process through analytical and simulation models, according to the ideal specification of the standard. However, measurements show that additional scanning gaps appear in the scanning process, which reduce the discovery capabilities. These gaps have been identified in all of the analyzed devices and respond to both regular patterns and variable events associated with the decoding process. We have demonstrated that these non-idealities, which are not taken into account in other studies, have a severe impact on the discovery process performance. Extensive performance evaluation for a varying number of devices and feasible parameter combinations has been done by comparing simulations and experimental measurements. This work also includes a simple mathematical model that closely matches both the standard implementation and the different chipset peculiarities for any possible parameter value specified in the standard and for any number of simultaneous advertising devices under scanner coverage.
On the reduced-complexity of LDPC decoders for ultra-high-speed optical transmission.
Djordjevic, Ivan B; Xu, Lei; Wang, Ting
2010-10-25
We propose two reduced-complexity (RC) LDPC decoders, which can be used in combination with large-girth LDPC codes to enable ultra-high-speed serial optical transmission. We show that optimally attenuated RC min-sum sum algorithm performs only 0.46 dB (at BER of 10(-9)) worse than conventional sum-product algorithm, while having lower storage memory requirements and much lower latency. We further study the use of RC LDPC decoding algorithms in multilevel coded modulation with coherent detection and show that with RC decoding algorithms we can achieve the net coding gain larger than 11 dB at BERs below 10(-9).
DEFF Research Database (Denmark)
Busk, Peter Kamp; Hallin, Peter Fischer; Salomon, Jesper
-regulatory elements. We have developed a method for identifying short, conserved motifs in biological sequences such as proteins, DNA and RNA5. This method was used for analysis of approximately 2000 Arabidopsis thaliana promoters that have been shown by DNA array analysis to be induced by abscisic acid6....... These promoters were compared to 28000 promoters that are not induced by abscisic acid. The analysis identified previously described ABA-inducible promoter elements such as ABRE, CE3 and CRT1 but also new cis-elements were found. Furthermore, the list of DNA elements could be used to predict ABA...
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.
Soft decoding a self-dual (48, 24; 12) code
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.