Competence in Streptococcus pneumoniae is regulated by the rate of ribosomal decoding errors.
Stevens, Kathleen E; Chang, Diana; Zwack, Erin E; Sebert, Michael E
2011-01-01
Competence for genetic transformation in Streptococcus pneumoniae develops in response to accumulation of a secreted peptide pheromone and was one of the initial examples of bacterial quorum sensing. Activation of this signaling system induces not only expression of the proteins required for transformation but also the production of cellular chaperones and proteases. We have shown here that activity of this pathway is sensitively responsive to changes in the accuracy of protein synthesis that are triggered by either mutations in ribosomal proteins or exposure to antibiotics. Increasing the error rate during ribosomal decoding promoted competence, while reducing the error rate below the baseline level repressed the development of both spontaneous and antibiotic-induced competence. This pattern of regulation was promoted by the bacterial HtrA serine protease. Analysis of strains with the htrA (S234A) catalytic site mutation showed that the proteolytic activity of HtrA selectively repressed competence when translational fidelity was high but not when accuracy was low. These findings redefine the pneumococcal competence pathway as a response to errors during protein synthesis. This response has the capacity to address the immediate challenge of misfolded proteins through production of chaperones and proteases and may also be able to address, through genetic exchange, upstream coding errors that cause intrinsic protein folding defects. The competence pathway may thereby represent a strategy for dealing with lesions that impair proper protein coding and for maintaining the coding integrity of the genome. The signaling pathway that governs competence in the human respiratory tract pathogen Streptococcus pneumoniae regulates both genetic transformation and the production of cellular chaperones and proteases. The current study shows that this pathway is sensitively controlled in response to changes in the accuracy of protein synthesis. Increasing the error rate during
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.
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.
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.
Mutational analysis of S12 protein and implications for the accuracy of decoding by the ribosome.
Sharma, Divya; Cukras, Anthony R; Rogers, Elizabeth J; Southworth, Daniel R; Green, Rachel
2007-12-07
The fidelity of aminoacyl-tRNA selection by the ribosome depends on a conformational switch in the decoding center of the small ribosomal subunit induced by cognate but not by near-cognate aminoacyl-tRNA. The aminoglycosides paromomycin and streptomycin bind to the decoding center and induce related structural rearrangements that explain their observed effects on miscoding. Structural and biochemical studies have identified ribosomal protein S12 (as well as specific nucleotides in 16S ribosomal RNA) as a critical molecular contributor in distinguishing between cognate and near-cognate tRNA species as well as in promoting more global rearrangements in the small subunit, referred to as "closure." Here we use a mutational approach to define contributions made by two highly conserved loops in S12 to the process of tRNA selection. Most S12 variant ribosomes tested display increased levels of fidelity (a "restrictive" phenotype). Interestingly, several variants, K42A and R53A, were substantially resistant to the miscoding effects of paromomycin. Further characterization of the compromised paromomycin response identified a probable second, fidelity-modulating binding site for paromomycin in the 16S ribosomal RNA that facilitates closure of the small subunit and compensates for defects associated with the S12 mutations.
New decoding methods of interleaved burst error-correcting codes
Nakano, Y.; Kasahara, M.; Namekawa, T.
1983-04-01
A probabilistic method of single burst error correction, using the syndrome correlation of subcodes which constitute the interleaved code, is presented. This method makes it possible to realize a high capability of burst error correction with less decoding delay. By generalizing this method it is possible to obtain probabilistic method of multiple (m-fold) burst error correction. After estimating the burst error positions using syndrome correlation of subcodes which are interleaved m-fold burst error detecting codes, this second method corrects erasure errors in each subcode and m-fold burst errors. The performance of these two methods is analyzed via computer simulation, and their effectiveness is demonstrated.
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...
Error-correction coding and decoding bounds, codes, decoders, analysis and applications
Tomlinson, Martin; Ambroze, Marcel A; Ahmed, Mohammed; Jibril, Mubarak
2017-01-01
This book discusses both the theory and practical applications of self-correcting data, commonly known as error-correcting codes. The applications included demonstrate the importance of these codes in a wide range of everyday technologies, from smartphones to secure communications and transactions. Written in a readily understandable style, the book presents the authors’ twenty-five years of research organized into five parts: Part I is concerned with the theoretical performance attainable by using error correcting codes to achieve communications efficiency in digital communications systems. Part II explores the construction of error-correcting codes and explains the different families of codes and how they are designed. Techniques are described for producing the very best codes. Part III addresses the analysis of low-density parity-check (LDPC) codes, primarily to calculate their stopping sets and low-weight codeword spectrum which determines the performance of these codes. Part IV deals with decoders desi...
A 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
Decoding of DBEC-TBED Reed-Solomon codes. [Double-Byte-Error-Correcting, Triple-Byte-Error-Detecting
Deng, Robert H.; Costello, Daniel J., Jr.
1987-01-01
A problem in designing semiconductor memories is to provide some measure of error control without requiring excessive coding overhead or decoding time. In LSI and VLSI technology, memories are often organized on a multiple bit (or byte) per chip basis. For example, some 256 K bit DRAM's are organized in 32 K x 8 bit-bytes. Byte-oriented codes such as Reed-Solomon (RS) codes can provide efficient low overhead error control for such memories. However, the standard iterative algorithm for decoding RS codes is too slow for these applications. The paper presents a special decoding technique for double-byte-error-correcting, triple-byte-error-detecting RS codes which is capable of high-speed operation. This technique is designed to find the error locations and the error values directly from the syndrome without having to use the iterative algorithm to find the error locator polynomial.
Massey, J. L.
1976-01-01
The very low error probability obtained with long error-correcting codes results in a very small number of observed errors in simulation studies of practical size and renders the usual confidence interval techniques inapplicable to the observed error probability. A natural extension of the notion of a 'confidence interval' is made and applied to such determinations of error probability by simulation. An example is included to show the surprisingly great significance of as few as two decoding errors in a very large number of decoding trials.
Euclidean Geometry Codes, minimum weight words and decodable error-patterns using bit-flipping
DEFF Research Database (Denmark)
Høholdt, Tom; Justesen, Jørn; Jonsson, Bergtor
2005-01-01
We determine the number of minimum wigth words in a class of Euclidean Geometry codes and link the performance of the bit-flipping decoding algorithm to the geometry of the error patterns.......We determine the number of minimum wigth words in a class of Euclidean Geometry codes and link the performance of the bit-flipping decoding algorithm to the geometry of the error patterns....
Fast decoding techniques for extended single-and-double-error-correcting Reed Solomon codes
Costello, D. J., Jr.; Deng, H.; Lin, S.
1984-01-01
A problem in designing semiconductor memories is to provide some measure of error control without requiring excessive coding overhead or decoding time. For example, some 256K-bit dynamic random access memories are organized as 32K x 8 bit-bytes. Byte-oriented codes such as Reed Solomon (RS) codes provide efficient low overhead error control for such memories. However, the standard iterative algorithm for decoding RS codes is too slow for these applications. Some special high speed decoding techniques for extended single and double error correcting RS codes. These techniques are designed to find the error locations and the error values directly from the syndrome without having to form the error locator polynomial and solve for its roots.
Remote one-qubit information concentration and decoding of operator quantum error-correction codes
International Nuclear Information System (INIS)
Hsu Liyi
2007-01-01
We propose the general scheme of remote one-qubit information concentration. To achieve the task, the Bell-correlated mixed states are exploited. In addition, the nonremote one-qubit information concentration is equivalent to the decoding of the quantum error-correction code. Here we propose how to decode the stabilizer codes. In particular, the proposed scheme can be used for the operator quantum error-correction codes. The encoded state can be recreated on the errorless qubit, regardless how many bit-flip errors and phase-flip errors have occurred
Probability of undetected error after decoding for a concatenated coding scheme
Costello, D. J., Jr.; Lin, S.
1984-01-01
A concatenated coding scheme for error control in data communications is analyzed. In this scheme, the inner code is used for both error correction and detection, however the outer code is used only for error detection. A retransmission is requested if the outer code detects the presence of errors after the inner code decoding. Probability of undetected error is derived and bounded. A particular example, proposed for NASA telecommand system is analyzed.
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.
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)
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.
Fast Erasure and Error decoding of Algebraic Geometry Codes up to the Feng-Rao Bound
DEFF Research Database (Denmark)
Jensen, Helge Elbrønd; Sakata, S.; Leonard, D.
1996-01-01
This paper gives an errata(that is erasure-and error-) decoding algorithm of one-point algebraic geometry codes up to the Feng-Rao designed minimum distance using Sakata's multidimensional generalization of the Berlekamp-massey algorithm and the votin procedure of Feng and Rao.......This paper gives an errata(that is erasure-and error-) decoding algorithm of one-point algebraic geometry codes up to the Feng-Rao designed minimum distance using Sakata's multidimensional generalization of the Berlekamp-massey algorithm and the votin procedure of Feng and Rao....
Quantum mean-field decoding algorithm for error-correcting codes
International Nuclear Information System (INIS)
Inoue, Jun-ichi; Saika, Yohei; Okada, Masato
2009-01-01
We numerically examine a quantum version of TAP (Thouless-Anderson-Palmer)-like mean-field algorithm for the problem of error-correcting codes. For a class of the so-called Sourlas error-correcting codes, we check the usefulness to retrieve the original bit-sequence (message) with a finite length. The decoding dynamics is derived explicitly and we evaluate the average-case performance through the bit-error rate (BER).
Dana, Alexandra; Tuller, Tamir
2014-12-01
Gene translation modeling and prediction is a fundamental problem that has numerous biomedical implementations. In this work we present a novel, user-friendly tool/index for calculating the mean of the typical decoding rates that enables predicting translation elongation efficiency of protein coding genes for different tissue types, developmental stages, and experimental conditions. The suggested translation efficiency index is based on the analysis of the organism's ribosome profiling data. This index could be used for example to predict changes in translation elongation efficiency of lowly expressed genes that usually have relatively low and/or biased ribosomal densities and protein levels measurements, or can be used for example for predicting translation efficiency of new genetically engineered genes. We demonstrate the usability of this index via the analysis of six organisms in different tissues and developmental stages. Distributable cross platform application and guideline are available for download at: http://www.cs.tau.ac.il/~tamirtul/MTDR/MTDR_Install.html. Copyright © 2015 Dana and Tuller.
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.
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.
Error-rate performance analysis of cooperative OFDMA system with decode-and-forward relaying
Fareed, Muhammad Mehboob; Uysal, Murat; Tsiftsis, Theodoros A.
2014-01-01
In this paper, we investigate the performance of a cooperative orthogonal frequency-division multiple-access (OFDMA) system with decode-and-forward (DaF) relaying. Specifically, we derive a closed-form approximate symbol-error-rate expression and analyze the achievable diversity orders. Depending on the relay location, a diversity order up to (LSkD + 1) + σ M m = 1 min(LSkRm + 1, LR mD + 1) is available, where M is the number of relays, and LS kD + 1, LSkRm + 1, and LRmD + 1 are the lengths of channel impulse responses of source-to-destination, source-to- mth relay, and mth relay-to-destination links, respectively. Monte Carlo simulation results are also presented to confirm the analytical findings. © 2013 IEEE.
Potts glass reflection of the decoding threshold for qudit quantum error correcting codes
Jiang, Yi; Kovalev, Alexey A.; Pryadko, Leonid P.
We map the maximum likelihood decoding threshold for qudit quantum error correcting codes to the multicritical point in generalized Potts gauge glass models, extending the map constructed previously for qubit codes. An n-qudit quantum LDPC code, where a qudit can be involved in up to m stabilizer generators, corresponds to a ℤd Potts model with n interaction terms which can couple up to m spins each. We analyze general properties of the phase diagram of the constructed model, give several bounds on the location of the transitions, bounds on the energy density of extended defects (non-local analogs of domain walls), and discuss the correlation functions which can be used to distinguish different phases in the original and the dual models. This research was supported in part by the Grants: NSF PHY-1415600 (AAK), NSF PHY-1416578 (LPP), and ARO W911NF-14-1-0272 (LPP).
Error-rate performance analysis of cooperative OFDMA system with decode-and-forward relaying
Fareed, Muhammad Mehboob
2014-06-01
In this paper, we investigate the performance of a cooperative orthogonal frequency-division multiple-access (OFDMA) system with decode-and-forward (DaF) relaying. Specifically, we derive a closed-form approximate symbol-error-rate expression and analyze the achievable diversity orders. Depending on the relay location, a diversity order up to (LSkD + 1) + σ M m = 1 min(LSkRm + 1, LR mD + 1) is available, where M is the number of relays, and LS kD + 1, LSkRm + 1, and LRmD + 1 are the lengths of channel impulse responses of source-to-destination, source-to- mth relay, and mth relay-to-destination links, respectively. Monte Carlo simulation results are also presented to confirm the analytical findings. © 2013 IEEE.
Fast Erasure-and error decoding of algebraic geometry codes up to the Feng-Rao bound
DEFF Research Database (Denmark)
Høholdt, Tom; Jensen, Helge Elbrønd; Sakata, Shojiro
1998-01-01
This correspondence gives an errata (that is erasure-and error-) decoding algorithm of one-point algebraic-geometry codes up to the Feng-Rao designed minimum distance using Sakata's multidimensional generalization of the Berlekamp-Massey algorithm and the voting procedure of Feng and Rao....
Decoding linear error-correcting codes up to half the minimum distance with Gröbner bases
Bulygin, S.; Pellikaan, G.R.; Sala, M.; Mora, T.; Perret, L.; Sakata, S.; Traverso, C.
2009-01-01
In this short note we show how one can decode linear error-correcting codes up to half the minimum distance via solving a system of polynomial equations over a finite field. We also explicitly present the reduced Gröbner basis for the system considered.
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
Bounded distance decoding of linear error-correcting codes with Gröbner bases
Bulygin, S.; Pellikaan, G.R.
2009-01-01
The problem of bounded distance decoding of arbitrary linear codes using Gröbner bases is addressed. A new method is proposed, which is based on reducing an initial decoding problem to solving a certain system of polynomial equations over a finite field. The peculiarity of this system is that, when
Toric Varieties and Codes, Error-correcting Codes, Quantum Codes, Secret Sharing and Decoding
DEFF Research Database (Denmark)
Hansen, Johan Peder
We present toric varieties and associated toric codes and their decoding. Toric codes are applied to construct Linear Secret Sharing Schemes (LSSS) with strong multiplication by the Massey construction. Asymmetric Quantum Codes are obtained from toric codes by the A.R. Calderbank P.W. Shor and A.......M. Steane construction of stabilizer codes (CSS) from linear codes containing their dual codes....
EEG-based decoding of error-related brain activity in a real-world driving task
Zhang, H.; Chavarriaga, R.; Khaliliardali, Z.; Gheorghe, L.; Iturrate, I.; Millán, J. d. R.
2015-12-01
Objectives. Recent studies have started to explore the implementation of brain-computer interfaces (BCI) as part of driving assistant systems. The current study presents an EEG-based BCI that decodes error-related brain activity. Such information can be used, e.g., to predict driver’s intended turning direction before reaching road intersections. Approach. We executed experiments in a car simulator (N = 22) and a real car (N = 8). While subject was driving, a directional cue was shown before reaching an intersection, and we classified the presence or not of an error-related potentials from EEG to infer whether the cued direction coincided with the subject’s intention. In this protocol, the directional cue can correspond to an estimation of the driving direction provided by a driving assistance system. We analyzed ERPs elicited during normal driving and evaluated the classification performance in both offline and online tests. Results. An average classification accuracy of 0.698 ± 0.065 was obtained in offline experiments in the car simulator, while tests in the real car yielded a performance of 0.682 ± 0.059. The results were significantly higher than chance level for all cases. Online experiments led to equivalent performances in both simulated and real car driving experiments. These results support the feasibility of decoding these signals to help estimating whether the driver’s intention coincides with the advice provided by the driving assistant in a real car. Significance. The study demonstrates a BCI system in real-world driving, extending the work from previous simulated studies. As far as we know, this is the first online study in real car decoding driver’s error-related brain activity. Given the encouraging results, the paradigm could be further improved by using more sophisticated machine learning approaches and possibly be combined with applications in intelligent vehicles.
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....
Error-rate performance analysis of incremental decode-and-forward opportunistic relaying
Tourki, Kamel; Yang, Hongchuan; Alouini, Mohamed-Slim
2011-01-01
In this paper, we investigate an incremental opportunistic relaying scheme where the selected relay chooses to cooperate only if the source-destination channel is of an unacceptable quality. In our study, we consider regenerative relaying in which the decision to cooperate is based on a signal-to-noise ratio (SNR) threshold and takes into account the effect of the possible erroneously detected and transmitted data at the best relay. We derive a closed-form expression for the end-to-end bit-error rate (BER) of binary phase-shift keying (BPSK) modulation based on the exact probability density function (PDF) of each hop. Furthermore, we evaluate the asymptotic error performance and the diversity order is deduced. We show that performance simulation results coincide with our analytical results. © 2011 IEEE.
Error-rate performance analysis of incremental decode-and-forward opportunistic relaying
Tourki, Kamel
2011-06-01
In this paper, we investigate an incremental opportunistic relaying scheme where the selected relay chooses to cooperate only if the source-destination channel is of an unacceptable quality. In our study, we consider regenerative relaying in which the decision to cooperate is based on a signal-to-noise ratio (SNR) threshold and takes into account the effect of the possible erroneously detected and transmitted data at the best relay. We derive a closed-form expression for the end-to-end bit-error rate (BER) of binary phase-shift keying (BPSK) modulation based on the exact probability density function (PDF) of each hop. Furthermore, we evaluate the asymptotic error performance and the diversity order is deduced. We show that performance simulation results coincide with our analytical results. © 2011 IEEE.
Error-rate performance analysis of incremental decode-and-forward opportunistic relaying
Tourki, Kamel; Yang, Hongchuan; Alouini, Mohamed-Slim
2010-01-01
In this paper, we investigate an incremental opportunistic relaying scheme where the selected relay chooses to cooperate only if the source-destination channel is of an unacceptable quality. In our study, we consider regenerative relaying in which the decision to cooperate is based on a signal-to-noise ratio (SNR) threshold and takes into account the effect of the possible erroneously detected and transmitted data at the best relay. We derive a closed-form expression for the end-to-end biterror rate (BER) of binary phase-shift keying (BPSK) modulation based on the exact probability density function (PDF) of each hop. Furthermore, we evaluate the asymptotic error performance and the diversity order is deduced. We show that performance simulation results coincide with our analytical results. ©2010 IEEE.
Error-rate performance analysis of incremental decode-and-forward opportunistic relaying
Tourki, Kamel
2010-10-01
In this paper, we investigate an incremental opportunistic relaying scheme where the selected relay chooses to cooperate only if the source-destination channel is of an unacceptable quality. In our study, we consider regenerative relaying in which the decision to cooperate is based on a signal-to-noise ratio (SNR) threshold and takes into account the effect of the possible erroneously detected and transmitted data at the best relay. We derive a closed-form expression for the end-to-end biterror rate (BER) of binary phase-shift keying (BPSK) modulation based on the exact probability density function (PDF) of each hop. Furthermore, we evaluate the asymptotic error performance and the diversity order is deduced. We show that performance simulation results coincide with our analytical results. ©2010 IEEE.
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.
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.
Sakata, Shojiro; Fujisawa, Masaya
It is a well-known fact [7], [9] that the BMS algorithm with majority voting can decode up to half the Feng-Rao designed distance dFR. Since dFR is not smaller than the Goppa designed distance dG, that algorithm can correct up to \\lfloor \\frac{d_G-1}{2}\\rfloor errors. On the other hand, it has been considered to be evident that the original BMS algorithm (without voting) [1], [2] can correct up to \\lfloor \\frac{d_G-g-1}{2}\\rfloor errors similarly to the basic algorithm by Skorobogatov-Vladut. But, is it true? In this short paper, we show that it is true, although we need a few remarks and some additional procedures for determining the Groebner basis of the error locator ideal exactly. In fact, as the basic algorithm gives a set of polynomials whose zero set contains the error locators as a subset, it cannot always give the exact error locators, unless the syndrome equation is solved to find the error values in addition.
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.
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.
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....
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....
Miscoding-induced stalling of substrate translocation on the bacterial ribosome.
Alejo, Jose L; Blanchard, Scott C
2017-10-10
Directional transit of the ribosome along the messenger RNA (mRNA) template is a key determinant of the rate and processivity of protein synthesis. Imaging of the multistep translocation mechanism using single-molecule FRET has led to the hypothesis that substrate movements relative to the ribosome resolve through relatively long-lived late intermediates wherein peptidyl-tRNA enters the P site of the small ribosomal subunit via reversible, swivel-like motions of the small subunit head domain within the elongation factor G (GDP)-bound ribosome complex. Consistent with translocation being rate-limited by recognition and productive engagement of peptidyl-tRNA within the P site, we now show that base-pairing mismatches between the peptidyl-tRNA anticodon and the mRNA codon dramatically delay this rate-limiting, intramolecular process. This unexpected relationship between aminoacyl-tRNA decoding and translocation suggests that miscoding antibiotics may impact protein synthesis by impairing the recognition of peptidyl-tRNA in the small subunit P site during EF-G-catalyzed translocation. Strikingly, we show that elongation factor P (EF-P), traditionally known to alleviate ribosome stalling at polyproline motifs, can efficiently rescue translocation defects arising from miscoding. These findings help reveal the nature and origin of the rate-limiting steps in substrate translocation on the bacterial ribosome and indicate that EF-P can aid in resuming translation elongation stalled by miscoding errors.
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....
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....
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.
Hoede, C.; Li, Z.
2001-01-01
In coding theory the problem of decoding focuses on error vectors. In the simplest situation code words are $(0,1)$-vectors, as are the received messages and the error vectors. Comparison of a received word with the code words yields a set of error vectors. In deciding on the original code word,
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.
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.
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)
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....
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,…
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).
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...
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.
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.
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
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.
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.
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
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; 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.
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 Ã¢Â€Âœturbo principleÃ¢Â€Â 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 Ã¢Â€ÂœconsensusÃ¢Â€Â 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.
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.
The Complete Structure of the Mycobacterium smegmatis 70S Ribosome
Directory of Open Access Journals (Sweden)
Jendrik Hentschel
2017-07-01
Full Text Available The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.
Resource Efficient LDPC Decoders for Multimedia Communication
Chandrasetty, Vikram Arkalgud; Aziz, Syed Mahfuzul
2013-01-01
Achieving high image quality is an important aspect in an increasing number of wireless multimedia applications. These applications require resource efficient error correction hardware to detect and correct errors introduced by the communication channel. This paper presents an innovative flexible architecture for error correction using Low-Density Parity-Check (LDPC) codes. The proposed partially-parallel decoder architecture utilizes a novel code construction technique based on multi-level H...
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 10Ã¢ÂˆÂ’6 at 2 dB over AWGN channel while performing maximum 18 decoding iterations.
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.
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.
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...
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...
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....
Video Error Correction Using Steganography
Robie, David L.; Mersereau, Russell M.
2002-12-01
The transmission of any data is always subject to corruption due to errors, but video transmission, because of its real time nature must deal with these errors without retransmission of the corrupted data. The error can be handled using forward error correction in the encoder or error concealment techniques in the decoder. This MPEG-2 compliant codec uses data hiding to transmit error correction information and several error concealment techniques in the decoder. The decoder resynchronizes more quickly with fewer errors than traditional resynchronization techniques. It also allows for perfect recovery of differentially encoded DCT-DC components and motion vectors. This provides for a much higher quality picture in an error-prone environment while creating an almost imperceptible degradation of the picture in an error-free environment.
Video Error Correction Using Steganography
Directory of Open Access Journals (Sweden)
Robie David L
2002-01-01
Full Text Available The transmission of any data is always subject to corruption due to errors, but video transmission, because of its real time nature must deal with these errors without retransmission of the corrupted data. The error can be handled using forward error correction in the encoder or error concealment techniques in the decoder. This MPEG-2 compliant codec uses data hiding to transmit error correction information and several error concealment techniques in the decoder. The decoder resynchronizes more quickly with fewer errors than traditional resynchronization techniques. It also allows for perfect recovery of differentially encoded DCT-DC components and motion vectors. This provides for a much higher quality picture in an error-prone environment while creating an almost imperceptible degradation of the picture in an error-free environment.
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.
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.
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.
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.
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).
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....
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.
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...
The Unexplored Mechanisms and Regulatory Functions of Ribosomal Translocation
Alejo, Jose Luis
In every cell, protein synthesis is carried out by the ribosome, a complex macromolecular RNA-protein assembly. Decades of structural and kinetic studies have increased our understanding of ribosome initiation, decoding, translocation and termination. Yet, the underlying mechanism of these fundamental processes has yet to be fully delineated. Hence, the molecular basis of regulation remains obscure. Here, single-molecule fluorescence methods are applied to decipher the mechanism and regulatory roles of the multi-step process of directional substrate translocation on the ribosome that accompanies every round of protein synthesis. In Chapter 1, single-molecule fluorescence resonance energy transfer (smFRET) is introduced as a tool for studying bacterial ribosome translocation. Chapter 2 details the experimental methods. In Chapter 3, the elongation factor G(EF-G)-catalyzed movement of substrates through the ribosome is examined from several perspectives or signals reporting on various degrees of freedom of ribosome dynamics. Two ribosomal states interconvert in the presence of EF-G(GDP), displaying novel head domain motions, until relocking takes place. In Chapter 4, in order to test if the mentioned fluctuations leading to relocking are correlated to the engagement of the P-site by the peptidyl-tRNA, the translocation of miscoded tRNAs is studied. Severe defects in the relocking stages of translocation reveal the correlation between this new stage of translocation and P-site tRNA engagement.
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....
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.
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
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....
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.
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.
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.
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.
Directory of Open Access Journals (Sweden)
Harold S Bernhardt
2015-11-01
Full Text Available It was Francis Crick who first asked why the ribosome contains so much RNA, and discussed the implications of this for the direct flow of genetic information from DNA to protein. Remarkable advances in our understanding of the ribosome and protein synthesis, including the recent publication of two mammalian mitochondrial ribosome structures, have shed new light on this intriguing aspect of evolution in molecular biology. We examine here whether RNA is indispensable for coded protein synthesis, or whether an all-protein ‘ribosome’ (or ‘synthosome’ might be possible, with a protein enzyme catalyzing peptide synthesis, and release factor-like protein adaptors able to read a message composed of deoxyribonucleotides. We also compare the RNA world hypothesis with the alternative ‘proteins first’ hypothesis in terms of their different understandings of the evolution of the ribosome, and whether this might have been preceded by an ancestral form of nonribosomal peptide synthesis catalyzed by protein enzymes.
Compact disk error measurements
Howe, D.; Harriman, K.; Tehranchi, B.
1993-01-01
The objectives of this project are as follows: provide hardware and software that will perform simple, real-time, high resolution (single-byte) measurement of the error burst and good data gap statistics seen by a photoCD player read channel when recorded CD write-once discs of variable quality (i.e., condition) are being read; extend the above system to enable measurement of the hard decision (i.e., 1-bit error flags) and soft decision (i.e., 2-bit error flags) decoding information that is produced/used by the Cross Interleaved - Reed - Solomon - Code (CIRC) block decoder employed in the photoCD player read channel; construct a model that uses data obtained via the systems described above to produce meaningful estimates of output error rates (due to both uncorrected ECC words and misdecoded ECC words) when a CD disc having specific (measured) error statistics is read (completion date to be determined); and check the hypothesis that current adaptive CIRC block decoders are optimized for pressed (DAD/ROM) CD discs. If warranted, do a conceptual design of an adaptive CIRC decoder that is optimized for write-once CD discs.
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.
Tensor Networks and Quantum Error Correction
Ferris, Andrew J.; Poulin, David
2014-07-01
We establish several relations between quantum error correction (QEC) and tensor network (TN) methods of quantum many-body physics. We exhibit correspondences between well-known families of QEC codes and TNs, and demonstrate a formal equivalence between decoding a QEC code and contracting a TN. We build on this equivalence to propose a new family of quantum codes and decoding algorithms that generalize and improve upon quantum polar codes and successive cancellation decoding in a natural way.
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
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
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.
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.
The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Hentschel, Jendrik; Burnside, Chloe; Mignot, Ingrid; Leibundgut, Marc; Boehringer, Daniel; Ban, Nenad
2017-07-05
The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.
The effect of tRNA levels on decoding times of mRNA codons.
Dana, Alexandra; Tuller, Tamir
2014-08-01
The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (-0.38 to -0.66, all P values decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
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.
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)
Genome-wide polysomal analysis of a yeast strain with mutated ribosomal protein S9
Directory of Open Access Journals (Sweden)
Arava Yoav
2007-08-01
Full Text Available Abstract Background The yeast ribosomal protein S9 (S9 is located at the entrance tunnel of the mRNA into the ribosome. It is known to play a role in accurate decoding and its bacterial homolog (S4 has recently been shown to be involved in opening RNA duplexes. Here we examined the effects of changing the C terminus of S9, which is rich in acidic amino acids and extends out of the ribosome surface. Results We performed a genome-wide analysis to reveal effects at the transcription and translation levels of all yeast genes. While negligible relative changes were observed in steady-state mRNA levels, a significant number of mRNAs appeared to have altered ribosomal density. Notably, 40% of the genes having reliable signals changed their ribosomal association by more than one ribosome. Yet, no general correlations with physical or functional features of the mRNA were observed. Ribosome Density Mapping (RDM along four of the mRNAs with increased association revealed an increase in ribosomal density towards the end of the coding region for at least two of them. Read-through analysis did not reveal any increase in read-through of a premature stop codon by the mutant strain. Conclusion The ribosomal protein rpS9 appears to be involved in the translation of many mRNAs, since altering its C terminus led to a significant change in ribosomal association of many mRNAs. We did not find strong correlations between these changes and several physical features of the mRNA, yet future studies with advanced tools may allow such correlations to be determined. Importantly, our results indicate an accumulation of ribosomes towards the end of the coding regions of some mRNAs. This suggests an involvement of S9 in ribosomal dissociation during translation termination.
Ribosomal Antibiotics: Contemporary Challenges
Directory of Open Access Journals (Sweden)
Tamar Auerbach-Nevo
2016-06-01
Full Text Available Most ribosomal antibiotics obstruct distinct ribosomal functions. In selected cases, in addition to paralyzing vital ribosomal tasks, some ribosomal antibiotics are involved in cellular regulation. Owing to the global rapid increase in the appearance of multi-drug resistance in pathogenic bacterial strains, and to the extremely slow progress in developing new antibiotics worldwide, it seems that, in addition to the traditional attempts at improving current antibiotics and the intensive screening for additional natural compounds, this field should undergo substantial conceptual revision. Here, we highlight several contemporary issues, including challenging the common preference of broad-range antibiotics; the marginal attention to alterations in the microbiome population resulting from antibiotics usage, and the insufficient awareness of ecological and environmental aspects of antibiotics usage. We also highlight recent advances in the identification of species-specific structural motifs that may be exploited for the design and the creation of novel, environmental friendly, degradable, antibiotic types, with a better distinction between pathogens and useful bacterial species in the microbiome. Thus, these studies are leading towards the design of “pathogen-specific antibiotics,” in contrast to the current preference of broad range antibiotics, partially because it requires significant efforts in speeding up the discovery of the unique species motifs as well as the clinical pathogen identification.
Expanding the ribosomal universe.
Dinman, Jonathan D; Kinzy, Terri Goss
2009-12-09
In this issue of Structure, Taylor et al. (2009) present the most complete model of an eukaryotic ribosome to date. This achievement represents a critical milestone along the path to structurally defining the unique aspects of the eukaryotic protein synthetic machinery.
Complete ML Decoding orf the (73,45) PG Code
DEFF Research Database (Denmark)
Justesen, Jørn; Høholdt, Tom; Hjaltason, Johan
2005-01-01
Our recent proof of the completeness of decoding by list bit flipping is reviewed. The proof is based on an enumeration of all cosets of low weight in terms of their minimum weight and syndrome weight. By using a geometric description of the error patterns we characterize all remaining cosets....
Adaptive Combined Source and Channel Decoding with Modulation ...
African Journals Online (AJOL)
In this paper, an adaptive system employing combined source and channel decoding with modulation is proposed for slow Rayleigh fading channels. Huffman code is used as the source code and Convolutional code is used for error control. The adaptive scheme employs a family of Convolutional codes of different rates ...
Fast decoding of codes from algebraic plane curves
DEFF Research Database (Denmark)
Justesen, Jørn; Larsen, Knud J.; Jensen, Helge Elbrønd
1992-01-01
Improvement to an earlier decoding algorithm for codes from algebraic geometry is presented. For codes from an arbitrary regular plane curve the authors correct up to d*/2-m2 /8+m/4-9/8 errors, where d* is the designed distance of the code and m is the degree of the curve. The complexity of finding...
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
Error-correction coding for digital communications
Clark, G. C., Jr.; Cain, J. B.
This book is written for the design engineer who must build the coding and decoding equipment and for the communication system engineer who must incorporate this equipment into a system. It is also suitable as a senior-level or first-year graduate text for an introductory one-semester course in coding theory. Fundamental concepts of coding are discussed along with group codes, taking into account basic principles, practical constraints, performance computations, coding bounds, generalized parity check codes, polynomial codes, and important classes of group codes. Other topics explored are related to simple nonalgebraic decoding techniques for group codes, soft decision decoding of block codes, algebraic techniques for multiple error correction, the convolutional code structure and Viterbi decoding, syndrome decoding techniques, and sequential decoding techniques. System applications are also considered, giving attention to concatenated codes, coding for the white Gaussian noise channel, interleaver structures for coded systems, and coding for burst noise channels.
Sudan-decoding generalized geometric Goppa codes
DEFF Research Database (Denmark)
Heydtmann, Agnes Eileen
2003-01-01
Generalized geometric Goppa codes are vector spaces of n-tuples with entries from different extension fields of a ground field. They are derived from evaluating functions similar to conventional geometric Goppa codes, but allowing evaluation in places of arbitrary degree. A decoding scheme...... for these codes based on Sudan's improved algorithm is presented and its error-correcting capacity is analyzed. For the implementation of the algorithm it is necessary that the so-called increasing zero bases of certain spaces of functions are available. A method to obtain such bases is developed....
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)
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.
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...
Modeling coherent errors in quantum error correction
Greenbaum, Daniel; Dutton, Zachary
2018-01-01
Analysis of quantum error correcting codes is typically done using a stochastic, Pauli channel error model for describing the noise on physical qubits. However, it was recently found that coherent errors (systematic rotations) on physical data qubits result in both physical and logical error rates that differ significantly from those predicted by a Pauli model. Here we examine the accuracy of the Pauli approximation for noise containing coherent errors (characterized by a rotation angle ɛ) under the repetition code. We derive an analytic expression for the logical error channel as a function of arbitrary code distance d and concatenation level n, in the small error limit. We find that coherent physical errors result in logical errors that are partially coherent and therefore non-Pauli. However, the coherent part of the logical error is negligible at fewer than {ε }-({dn-1)} error correction cycles when the decoder is optimized for independent Pauli errors, thus providing a regime of validity for the Pauli approximation. Above this number of correction cycles, the persistent coherent logical error will cause logical failure more quickly than the Pauli model would predict, and this may need to be combated with coherent suppression methods at the physical level or larger codes.
Maximum likelihood convolutional decoding (MCD) performance due to system losses
Webster, L.
1976-01-01
A model for predicting the computational performance of a maximum likelihood convolutional decoder (MCD) operating in a noisy carrier reference environment is described. This model is used to develop a subroutine that will be utilized by the Telemetry Analysis Program to compute the MCD bit error rate. When this computational model is averaged over noisy reference phase errors using a high-rate interpolation scheme, the results are found to agree quite favorably with experimental measurements.
Fast Transform Decoding Of Nonsystematic Reed-Solomon Codes
Truong, Trieu-Kie; Cheung, Kar-Ming; Shiozaki, A.; Reed, Irving S.
1992-01-01
Fast, efficient Fermat number transform used to compute F'(x) analogous to computation of syndrome in conventional decoding scheme. Eliminates polynomial multiplications and reduces number of multiplications in reconstruction of F'(x) to n log (n). Euclidean algorithm used to evaluate F(x) directly, without going through intermediate steps of solving error-locator and error-evaluator polynomials. Algorithm suitable for implementation in very-large-scale integrated circuits.
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.
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-...
Bogler, Carsten; Mehnert, Jan; Steinbrink, Jens; Haynes, John-Dylan
2014-01-01
Sustained, long-term cognitive workload is associated with variations and decrements in performance. Such fluctuations in vigilance can be a risk factor especially during dangerous attention demanding activities. Functional MRI studies have shown that attentional performance is correlated with BOLD-signals, especially in parietal and prefrontal cortical regions. An interesting question is whether these BOLD-signals could be measured in real-world scenarios, say to warn in a dangerous workplace whenever a subjects' vigilance is low. Because fMRI lacks the mobility needed for such applications, we tested whether the monitoring of vigilance might be possible using Near-Infrared Spectroscopy (NIRS). NIRS is a highly mobile technique that measures hemodynamics in the surface of the brain. We demonstrate that non-invasive NIRS signals correlate with vigilance. These signals carry enough information to decode subjects' reaction times at a single trial level.
Directory of Open Access Journals (Sweden)
Carsten Bogler
Full Text Available Sustained, long-term cognitive workload is associated with variations and decrements in performance. Such fluctuations in vigilance can be a risk factor especially during dangerous attention demanding activities. Functional MRI studies have shown that attentional performance is correlated with BOLD-signals, especially in parietal and prefrontal cortical regions. An interesting question is whether these BOLD-signals could be measured in real-world scenarios, say to warn in a dangerous workplace whenever a subjects' vigilance is low. Because fMRI lacks the mobility needed for such applications, we tested whether the monitoring of vigilance might be possible using Near-Infrared Spectroscopy (NIRS. NIRS is a highly mobile technique that measures hemodynamics in the surface of the brain. We demonstrate that non-invasive NIRS signals correlate with vigilance. These signals carry enough information to decode subjects' reaction times at a single trial level.
Astrophysics Decoding the cosmos
Irwin, Judith A
2007-01-01
Astrophysics: Decoding the Cosmos is an accessible introduction to the key principles and theories underlying astrophysics. This text takes a close look at the radiation and particles that we receive from astronomical objects, providing a thorough understanding of what this tells us, drawing the information together using examples to illustrate the process of astrophysics. Chapters dedicated to objects showing complex processes are written in an accessible manner and pull relevant background information together to put the subject firmly into context. The intention of the author is that the book will be a 'tool chest' for undergraduate astronomers wanting to know the how of astrophysics. Students will gain a thorough grasp of the key principles, ensuring that this often-difficult subject becomes more accessible.
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.
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...
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.
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.
Directory of Open Access Journals (Sweden)
Jeffrey A Hussmann
2015-12-01
Full Text Available Ribosome profiling produces snapshots of the locations of actively translating ribosomes on messenger RNAs. These snapshots can be used to make inferences about translation dynamics. Recent ribosome profiling studies in yeast, however, have reached contradictory conclusions regarding the average translation rate of each codon. Some experiments have used cycloheximide (CHX to stabilize ribosomes before measuring their positions, and these studies all counterintuitively report a weak negative correlation between the translation rate of a codon and the abundance of its cognate tRNA. In contrast, some experiments performed without CHX report strong positive correlations. To explain this contradiction, we identify unexpected patterns in ribosome density downstream of each type of codon in experiments that use CHX. These patterns are evidence that elongation continues to occur in the presence of CHX but with dramatically altered codon-specific elongation rates. The measured positions of ribosomes in these experiments therefore do not reflect the amounts of time ribosomes spend at each position in vivo. These results suggest that conclusions from experiments in yeast using CHX may need reexamination. In particular, we show that in all such experiments, codons decoded by less abundant tRNAs were in fact being translated more slowly before the addition of CHX disrupted these dynamics.
In vitro degradation of ribosomes.
Mora, G; Rivas, A
1976-12-01
The cytoplasmic ribosomes from Euglena gracilis var. bacillaris are found to be of two types taking into consideration their stability "in vitro". In the group of unstable ribosomes the large subunit is degraded. The other group apparently does not suffer any degradation under the conditions described. However the RNAs extracted from both types of ribosomes are degraded during sucrose density gradients. The degradation of the largest RNA species has been reported previously, but no comment has been made about the stability of the ribosome itself.
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.
International Nuclear Information System (INIS)
Otaka, E.; Kobata, K.
1978-01-01
The cytoplasmic 80s ribosomal proteins from the cells of yeast Saccharomyces cerevisiae were analyzed by SDS two-dimensional polyacrylamide gel electrophoresis. Seventyfour proteins were identified and consecutively numbered from 1 to 74. Upon oxidation of the 80s proteins with performic acid, ten proteins (no. 15, 20, 35, 40, 44, 46, 49, 51, 54 and 55) were dislocated on the gel without change of the total number of protein spots. Five proteins (no. 8, 14, 16, 36 and 74) were phosphorylated in vivo as seen in 32 P-labelling experiments. The large and small subunits separated in low magnesium medium were analyzed by the above gel electrophoresis. At least forty-five and twenty-eight proteins were assumed to be in the large and small subunits, respectively. All proteins found in the 80s ribosomes, except for no. 3, were detected in either subunit without appearance of new spots. The acidic protein no. 3 seems to be lost during subunit dissociation. (orig.) [de
Directory of Open Access Journals (Sweden)
Liu Yu-Sun
2011-01-01
Full Text Available Abstract The performance of the wrap-around Viterbi decoding algorithm with finite truncation depth and fixed decoding trellis length is investigated for tail-biting convolutional codes in the mobile WiMAX standard. Upper bounds on the error probabilities induced by finite truncation depth and the uncertainty of the initial state are derived for the AWGN channel. The truncation depth and the decoding trellis length that yield negligible performance loss are obtained for all transmission rates over the Rayleigh channel using computer simulations. The results show that the circular decoding algorithm with an appropriately chosen truncation depth and a decoding trellis just a fraction longer than the original received code words can achieve almost the same performance as the optimal maximum likelihood decoding algorithm in mobile WiMAX. A rule of thumb for the values of the truncation depth and the trellis tail length is also proposed.
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.
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.
Decoding suprathreshold stochastic resonance with optimal weights
International Nuclear Information System (INIS)
Xu, Liyan; Vladusich, Tony; Duan, Fabing; Gunn, Lachlan J.; Abbott, Derek; McDonnell, Mark D.
2015-01-01
We investigate an array of stochastic quantizers for converting an analog input signal into a discrete output in the context of suprathreshold stochastic resonance. A new optimal weighted decoding is considered for different threshold level distributions. We show that for particular noise levels and choices of the threshold levels optimally weighting the quantizer responses provides a reduced mean square error in comparison with the original unweighted array. However, there are also many parameter regions where the original array provides near optimal performance, and when this occurs, it offers a much simpler approach than optimally weighting each quantizer's response. - Highlights: • A weighted summing array of independently noisy binary comparators is investigated. • We present an optimal linearly weighted decoding scheme for combining the comparator responses. • We solve for the optimal weights by applying least squares regression to simulated data. • We find that the MSE distortion of weighting before summation is superior to unweighted summation of comparator responses. • For some parameter regions, the decrease in MSE distortion due to weighting is negligible
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.
Unitary Application of the Quantum Error Correction Codes
International Nuclear Information System (INIS)
You Bo; Xu Ke; Wu Xiaohua
2012-01-01
For applying the perfect code to transmit quantum information over a noise channel, the standard protocol contains four steps: the encoding, the noise channel, the error-correction operation, and the decoding. In present work, we show that this protocol can be simplified. The error-correction operation is not necessary if the decoding is realized by the so-called complete unitary transformation. We also offer a quantum circuit, which can correct the arbitrary single-qubit errors.
DEFF Research Database (Denmark)
Martinez Peñas, Umberto; Pellikaan, Ruud
2017-01-01
Error-correcting pairs were introduced as a general method of decoding linear codes with respect to the Hamming metric using coordinatewise products of vectors, and are used for many well-known families of codes. In this paper, we define new types of vector products, extending the coordinatewise ...
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.
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...
Performance analysis of a decoding algorithm for algebraic-geometry codes
DEFF Research Database (Denmark)
Høholdt, Tom; Jensen, Helge Elbrønd; Nielsen, Rasmus Refslund
1999-01-01
The fast decoding algorithm for one point algebraic-geometry codes of Sakata, Elbrond Jensen, and Hoholdt corrects all error patterns of weight less than half the Feng-Rao minimum distance. In this correspondence we analyze the performance of the algorithm for heavier error patterns. It turns out...
Indian Academy of Sciences (India)
having a probability Pi of being equal to a 1. Let us assume ... equal to a 0/1 has no bearing on the probability of the. It is often ... bits (call this set S) whose individual bits add up to zero ... In the context of binary error-correct~ng codes, specifi-.
Erales, Jenny; Marchand, Virginie; Panthu, Baptiste; Gillot, Sandra; Belin, Stéphane; Ghayad, Sandra E; Garcia, Maxime; Laforêts, Florian; Marcel, Virginie; Baudin-Baillieu, Agnès; Bertin, Pierre; Couté, Yohann; Adrait, Annie; Meyer, Mélanie; Therizols, Gabriel; Yusupov, Marat; Namy, Olivier; Ohlmann, Théophile; Motorin, Yuri; Catez, Frédéric; Diaz, Jean-Jacques
2017-12-05
Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells. Using RiboMethSeq, a nonbiased quantitative mapping of 2'-O-Me, we identified a repertoire of 2'-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2'-O-Me plasticity. Using the cricket paralysis virus internal ribosome entry site element, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through a 2'-O-Me pattern and not by nonribosomal actors of the translational machinery. Our data establish rRNA 2'-O-Me plasticity as a mechanism providing functional specificity to human ribosomes.
Cross-linking of streptomycin to the 16S ribosomal RNA of Escherichia coli
International Nuclear Information System (INIS)
Gravel, M.; Melancon, P.; Barkier-Gingras, L.
1987-01-01
[ 3 H]Dihydrostreptomycin was cross-linked to the 30S ribosomal subunit from Escherichia coli with the bifunctional reagent nitrogen mustard. The cross-linking primarily involved the 16S RNA. To localize the site of cross-linking of streptomycin to the 16S RNA, the authors hybridized RNA labeled with streptomycin to restriction fragments of the 16S RNA gene. Labeled RNA hybridized to DNA fragments corresponding to bases 892-917 and bases 1394-1415. These two segments of the ribosomal RNA must by juxtaposed in the ribosome, since there is a single binding site for streptomycin. This region has been implicated both in the decoding site and in the binding of initiation factor IF-3, indicating its functional importance
Efficient algorithms for maximum likelihood decoding in the surface code
Bravyi, Sergey; Suchara, Martin; Vargo, Alexander
2014-09-01
We describe two implementations of the optimal error correction algorithm known as the maximum likelihood decoder (MLD) for the two-dimensional surface code with a noiseless syndrome extraction. First, we show how to implement MLD exactly in time O (n2), where n is the number of code qubits. Our implementation uses a reduction from MLD to simulation of matchgate quantum circuits. This reduction however requires a special noise model with independent bit-flip and phase-flip errors. Secondly, we show how to implement MLD approximately for more general noise models using matrix product states (MPS). Our implementation has running time O (nχ3), where χ is a parameter that controls the approximation precision. The key step of our algorithm, borrowed from the density matrix renormalization-group method, is a subroutine for contracting a tensor network on the two-dimensional grid. The subroutine uses MPS with a bond dimension χ to approximate the sequence of tensors arising in the course of contraction. We benchmark the MPS-based decoder against the standard minimum weight matching decoder observing a significant reduction of the logical error probability for χ ≥4.
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...
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...
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...
Error correcting coding for OTN
DEFF Research Database (Denmark)
Justesen, Jørn; Larsen, Knud J.; Pedersen, Lars A.
2010-01-01
Forward error correction codes for 100 Gb/s optical transmission are currently receiving much attention from transport network operators and technology providers. We discuss the performance of hard decision decoding using product type codes that cover a single OTN frame or a small number...... of such frames. In particular we argue that a three-error correcting BCH is the best choice for the component code in such 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.
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
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.
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
Iterative optimization of quantum error correcting codes
International Nuclear Information System (INIS)
Reimpell, M.; Werner, R.F.
2005-01-01
We introduce a convergent iterative algorithm for finding the optimal coding and decoding operations for an arbitrary noisy quantum channel. This algorithm does not require any error syndrome to be corrected completely, and hence also finds codes outside the usual Knill-Laflamme definition of error correcting codes. The iteration is shown to improve the figure of merit 'channel fidelity' in every step
The ribosome uses two active mechanisms to unwind messenger RNA during translation.
Qu, Xiaohui; Wen, Jin-Der; Lancaster, Laura; Noller, Harry F; Bustamante, Carlos; Tinoco, Ignacio
2011-07-06
The ribosome translates the genetic information encoded in messenger RNA into protein. Folded structures in the coding region of an mRNA represent a kinetic barrier that lowers the peptide elongation rate, as the ribosome must disrupt structures it encounters in the mRNA at its entry site to allow translocation to the next codon. Such structures are exploited by the cell to create diverse strategies for translation regulation, such as programmed frameshifting, the modulation of protein expression levels, ribosome localization and co-translational protein folding. Although strand separation activity is inherent to the ribosome, requiring no exogenous helicases, its mechanism is still unknown. Here, using a single-molecule optical tweezers assay on mRNA hairpins, we find that the translation rate of identical codons at the decoding centre is greatly influenced by the GC content of folded structures at the mRNA entry site. Furthermore, force applied to the ends of the hairpin to favour its unfolding significantly speeds translation. Quantitative analysis of the force dependence of its helicase activity reveals that the ribosome, unlike previously studied helicases, uses two distinct active mechanisms to unwind mRNA structure: it destabilizes the helical junction at the mRNA entry site by biasing its thermal fluctuations towards the open state, increasing the probability of the ribosome translocating unhindered; and it mechanically pulls apart the mRNA single strands of the closed junction during the conformational changes that accompany ribosome translocation. The second of these mechanisms ensures a minimal basal rate of translation in the cell; specialized, mechanically stable structures are required to stall the ribosome temporarily. Our results establish a quantitative mechanical basis for understanding the mechanism of regulation of the elongation rate of translation by structured mRNAs. ©2011 Macmillan Publishers Limited. All rights reserved
The SmpB C-terminal tail helps tmRNA to recognize and enter stalled ribosomes
Directory of Open Access Journals (Sweden)
Mickey R. Miller
2014-09-01
Full Text Available In bacteria, transfer-messenger RNA (tmRNA and SmpB comprise the most common and effective system for rescuing stalled ribosomes. Ribosomes stall on mRNA transcripts lacking stop codons and are rescued as the defective mRNA is swapped for the tmRNA template in a process known as trans-translation. The tmRNA–SmpB complex is recruited to the ribosome independent of a codon–anticodon interaction. Given that the ribosome uses robust discriminatory mechanisms to select against non-cognate tRNAs during canonical decoding, it has been hard to explain how this can happen. Recent structural and biochemical studies show that SmpB licenses tmRNA entry through its interactions with the decoding center and mRNA channel. In particular, the C-terminal tail of SmpB promotes both EFTu activation and accommodation of tmRNA, the former through interactions with 16S rRNA nucleotide G530 and the latter through interactions with the mRNA channel downstream of the A site. Here we present a detailed model of the earliest steps in trans-translation, and in light of these mechanistic considerations, revisit the question of how tmRNA preferentially reacts with stalled, non-translating ribosomes.
Effect of mutations in the A site of 16 S rRNA on aminoglycoside antibiotic-ribosome interaction
DEFF Research Database (Denmark)
Recht, M I; Douthwaite, S; Dahlquist, K D
1999-01-01
antibiotics, which also interact with this region of rRNA. Mutations of certain nucleotides in rRNA reduce aminoglycoside binding affinity, as previously demonstrated using a model RNA oligonucleotide system. Here, predictions from the oligonucleotide system were tested in the ribosome by mutation...... for the aminoglycoside paromomycin, whereas no discernible reduction in affinity was observed with 1406 mutant ribosomes. These data are consistent with prior NMR structural determination of aminoglycoside interaction with the decoding region, and further our understanding of how aminoglycoside resistance can...
Neuron-Like Networks Between Ribosomal Proteins Within the Ribosome
Poirot, Olivier; Timsit, Youri
2016-05-01
From brain to the World Wide Web, information-processing networks share common scale invariant properties. Here, we reveal the existence of neural-like networks at a molecular scale within the ribosome. We show that with their extensions, ribosomal proteins form complex assortative interaction networks through which they communicate through tiny interfaces. The analysis of the crystal structures of 50S eubacterial particles reveals that most of these interfaces involve key phylogenetically conserved residues. The systematic observation of interactions between basic and aromatic amino acids at the interfaces and along the extension provides new structural insights that may contribute to decipher the molecular mechanisms of signal transmission within or between the ribosomal proteins. Similar to neurons interacting through “molecular synapses”, ribosomal proteins form a network that suggest an analogy with a simple molecular brain in which the “sensory-proteins” innervate the functional ribosomal sites, while the “inter-proteins” interconnect them into circuits suitable to process the information flow that circulates during protein synthesis. It is likely that these circuits have evolved to coordinate both the complex macromolecular motions and the binding of the multiple factors during translation. This opens new perspectives on nanoscale information transfer and processing.
Codes on the Klein quartic, ideals, and decoding
DEFF Research Database (Denmark)
Hansen, Johan P.
1987-01-01
descriptions as left ideals in the group-algebra GF(2^{3})[G]. This description allows for easy decoding. For instance, in the case of the single error correcting code of length21and dimension16with minimal distance3. decoding is obtained by multiplication with an idempotent in the group algebra.......A sequence of codes with particular symmetries and with large rates compared to their minimal distances is constructed over the field GF(2^{3}). In the sequence there is, for instance, a code of length 21 and dimension10with minimal distance9, and a code of length21and dimension16with minimal...... distance3. The codes are constructed from algebraic geometry using the dictionary between coding theory and algebraic curves over finite fields established by Goppa. The curve used in the present work is the Klein quartic. This curve has the maximal number of rational points over GF(2^{3})allowed by Serre...
[Efficacy of decoding training for children with difficulty reading hiragana].
Uchiyama, Hitoshi; Tanaka, Daisuke; Seki, Ayumi; Wakamiya, Eiji; Hirasawa, Noriko; Iketani, Naotake; Kato, Ken; Koeda, Tatsuya
2013-05-01
The present study aimed to clarify the efficacy of decoding training focusing on the correspondence between written symbols and their readings for children with difficulty reading hiragana (Japanese syllabary). Thirty-five children with difficulty reading hiragana were selected from among 367 first-grade elementary school students using a reading aloud test and were then divided into intervention (n=15) and control (n=20) groups. The intervention comprised 5 minutes of decoding training each day for a period of 3 weeks using an original program on a personal computer. Reading time and number of reading errors in the reading aloud test were compared between the groups. The intervention group showed a significant shortening of reading time (F(1,33)=5.40, phiragana.
Sum of the Magnitude for Hard Decision Decoding Algorithm Based on Loop Update Detection
Meng, Jiahui; Zhao, Danfeng; Tian, Hai; Zhang, Liang
2018-01-01
In order to improve the performance of non-binary low-density parity check codes (LDPC) hard decision decoding algorithm and to reduce the complexity of decoding, a sum of the magnitude for hard decision decoding algorithm based on loop update detection is proposed. This will also ensure the reliability, stability and high transmission rate of 5G mobile communication. The algorithm is based on the hard decision decoding algorithm (HDA) and uses the soft information from the channel to calculate the reliability, while the sum of the variable nodes’ (VN) magnitude is excluded for computing the reliability of the parity checks. At the same time, the reliability information of the variable node is considered and the loop update detection algorithm is introduced. The bit corresponding to the error code word is flipped multiple times, before this is searched in the order of most likely error probability to finally find the correct code word. Simulation results show that the performance of one of the improved schemes is better than the weighted symbol flipping (WSF) algorithm under different hexadecimal numbers by about 2.2 dB and 2.35 dB at the bit error rate (BER) of 10−5 over an additive white Gaussian noise (AWGN) channel, respectively. Furthermore, the average number of decoding iterations is significantly reduced. PMID:29342963
Sum of the Magnitude for Hard Decision Decoding Algorithm Based on Loop Update Detection.
Meng, Jiahui; Zhao, Danfeng; Tian, Hai; Zhang, Liang
2018-01-15
In order to improve the performance of non-binary low-density parity check codes (LDPC) hard decision decoding algorithm and to reduce the complexity of decoding, a sum of the magnitude for hard decision decoding algorithm based on loop update detection is proposed. This will also ensure the reliability, stability and high transmission rate of 5G mobile communication. The algorithm is based on the hard decision decoding algorithm (HDA) and uses the soft information from the channel to calculate the reliability, while the sum of the variable nodes' (VN) magnitude is excluded for computing the reliability of the parity checks. At the same time, the reliability information of the variable node is considered and the loop update detection algorithm is introduced. The bit corresponding to the error code word is flipped multiple times, before this is searched in the order of most likely error probability to finally find the correct code word. Simulation results show that the performance of one of the improved schemes is better than the weighted symbol flipping (WSF) algorithm under different hexadecimal numbers by about 2.2 dB and 2.35 dB at the bit error rate (BER) of 10 -5 over an additive white Gaussian noise (AWGN) channel, respectively. Furthermore, the average number of decoding iterations is significantly reduced.
Sum of the Magnitude for Hard Decision Decoding Algorithm Based on Loop Update Detection
Directory of Open Access Journals (Sweden)
Jiahui Meng
2018-01-01
Full Text Available In order to improve the performance of non-binary low-density parity check codes (LDPC hard decision decoding algorithm and to reduce the complexity of decoding, a sum of the magnitude for hard decision decoding algorithm based on loop update detection is proposed. This will also ensure the reliability, stability and high transmission rate of 5G mobile communication. The algorithm is based on the hard decision decoding algorithm (HDA and uses the soft information from the channel to calculate the reliability, while the sum of the variable nodes’ (VN magnitude is excluded for computing the reliability of the parity checks. At the same time, the reliability information of the variable node is considered and the loop update detection algorithm is introduced. The bit corresponding to the error code word is flipped multiple times, before this is searched in the order of most likely error probability to finally find the correct code word. Simulation results show that the performance of one of the improved schemes is better than the weighted symbol flipping (WSF algorithm under different hexadecimal numbers by about 2.2 dB and 2.35 dB at the bit error rate (BER of 10−5 over an additive white Gaussian noise (AWGN channel, respectively. Furthermore, the average number of decoding iterations is significantly reduced.
Observing human movements helps decoding environmental forces.
Zago, Myrka; La Scaleia, Barbara; Miller, William L; Lacquaniti, Francesco
2011-11-01
Vision of human actions can affect several features of visual motion processing, as well as the motor responses of the observer. Here, we tested the hypothesis that action observation helps decoding environmental forces during the interception of a decelerating target within a brief time window, a task intrinsically very difficult. We employed a factorial design to evaluate the effects of scene orientation (normal or inverted) and target gravity (normal or inverted). Button-press triggered the motion of a bullet, a piston, or a human arm. We found that the timing errors were smaller for upright scenes irrespective of gravity direction in the Bullet group, while the errors were smaller for the standard condition of normal scene and gravity in the Piston group. In the Arm group, instead, performance was better when the directions of scene and target gravity were concordant, irrespective of whether both were upright or inverted. These results suggest that the default viewer-centered reference frame is used with inanimate scenes, such as those of the Bullet and Piston protocols. Instead, the presence of biological movements in animate scenes (as in the Arm protocol) may help processing target kinematics under the ecological conditions of coherence between scene and target gravity directions.
Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis.
Boehringer, Daniel; O'Farrell, Heather C; Rife, Jason P; Ban, Nenad
2012-03-23
The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3'-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation.
Structural Insights into Methyltransferase KsgA Function in 30S Ribosomal Subunit Biogenesis*
Boehringer, Daniel; O'Farrell, Heather C.; Rife, Jason P.; Ban, Nenad
2012-01-01
The assembly of the ribosomal subunits is facilitated by ribosome biogenesis factors. The universally conserved methyltransferase KsgA modifies two adjacent adenosine residues in the 3′-terminal helix 45 of the 16 S ribosomal RNA (rRNA). KsgA recognizes its substrate adenosine residues only in the context of a near mature 30S subunit and is required for the efficient processing of the rRNA termini during ribosome biogenesis. Here, we present the cryo-EM structure of KsgA bound to a nonmethylated 30S ribosomal subunit. The structure reveals that KsgA binds to the 30S platform with the catalytic N-terminal domain interacting with substrate adenosine residues in helix 45 and the C-terminal domain making extensive contacts to helix 27 and helix 24. KsgA excludes the penultimate rRNA helix 44 from adopting its position in the mature 30S subunit, blocking the formation of the decoding site and subunit joining. We suggest that the activation of methyltransferase activity and subsequent dissociation of KsgA control conformational changes in helix 44 required for final rRNA processing and translation initiation. PMID:22308031
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.
Atkins, John F; Loughran, Gary; Bhatt, Pramod R; Firth, Andrew E; Baranov, Pavel V
2016-09-06
Genetic decoding is not 'frozen' as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational 'correction' of problem or 'savior' indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5' or 3' of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3' from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
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....
Statistical mechanics of error-correcting codes
Kabashima, Y.; Saad, D.
1999-01-01
We investigate the performance of error-correcting codes, where the code word comprises products of K bits selected from the original message and decoding is carried out utilizing a connectivity tensor with C connections per index. Shannon's bound for the channel capacity is recovered for large K and zero temperature when the code rate K/C is finite. Close to optimal error-correcting capability is obtained for finite K and C. We examine the finite-temperature case to assess the use of simulated annealing for decoding and extend the analysis to accommodate other types of noisy channels.
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.
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
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.
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
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...
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....
Performance analysis of linear codes under maximum-likelihood decoding: a tutorial
National Research Council Canada - National Science Library
Sason, Igal; Shamai, Shlomo
2006-01-01
..., upper and lower bounds on the error probability of linear codes under ML decoding are surveyed and applied to codes and ensembles of codes on graphs. For upper bounds, we discuss various bounds where focus is put on Gallager bounding techniques and their relation to a variety of other reported bounds. Within the class of lower bounds, we ad...
Restoring the Generalizability of SVM Based Decoding in High Dimensional Neuroimage Data
DEFF Research Database (Denmark)
Abrahamsen, Trine Julie; Hansen, Lars Kai
2011-01-01
Variance inflation is caused by a mismatch between linear projections of test and training data when projections are estimated on training sets smaller than the dimensionality of the feature space. We demonstrate that variance inflation can lead to an increased neuroimage decoding error rate...
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.
An LDPC decoder architecture for wireless sensor network applications.
Biroli, Andrea Dario Giancarlo; Martina, Maurizio; Masera, Guido
2012-01-01
The pervasive use of wireless sensors in a growing spectrum of human activities reinforces the need for devices with low energy dissipation. In this work, coded communication between a couple of wireless sensor devices is considered as a method to reduce the dissipated energy per transmitted bit with respect to uncoded communication. Different Low Density Parity Check (LDPC) codes are considered to this purpose and post layout results are shown for a low-area low-energy decoder, which offers percentage energy savings with respect to the uncoded solution in the range of 40%-80%, depending on considered environment, distance and bit error rate.
An LDPC Decoder Architecture for Wireless Sensor Network Applications
Giancarlo Biroli, Andrea Dario; Martina, Maurizio; Masera, Guido
2012-01-01
The pervasive use of wireless sensors in a growing spectrum of human activities reinforces the need for devices with low energy dissipation. In this work, coded communication between a couple of wireless sensor devices is considered as a method to reduce the dissipated energy per transmitted bit with respect to uncoded communication. Different Low Density Parity Check (LDPC) codes are considered to this purpose and post layout results are shown for a low-area low-energy decoder, which offers percentage energy savings with respect to the uncoded solution in the range of 40%–80%, depending on considered environment, distance and bit error rate. PMID:22438724
A Novel Modified Algorithm with Reduced Complexity LDPC Code Decoder
Directory of Open Access Journals (Sweden)
Song Yang
2014-10-01
Full Text Available A novel efficient decoding algorithm reduced the sum-product algorithm (SPA Complexity with LPDC code is proposed. Base on the hyperbolic tangent rule, modified the Check node update with two horizontal process, which have similar calculation, Motivated by the finding that sun- min (MS algorithm reduce the complexity reducing the approximation error in the horizontal process, simplify the information weight small part. Compared with the exiting approximations, the proposed method is less computational complexity than SPA algorithm. Simulation results show that the author algorithm can achieve performance very close SPA.
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.)
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)
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...
MATHEMATICAL AND COMPUTATIONAL MODELLING OF RIBOSOMAL MOVEMENT AND PROTEIN SYNTHESIS: AN OVERVIEW
Directory of Open Access Journals (Sweden)
Tobias von der Haar
2012-04-01
Full Text Available Translation or protein synthesis consists of a complex system of chemical reactions, which ultimately result in decoding of the mRNA and the production of a protein. The complexity of this reaction system makes it difficult to quantitatively connect its input parameters (such as translation factor or ribosome concentrations, codon composition of the mRNA, or energy availability to output parameters (such as protein synthesis rates or ribosome densities on mRNAs. Mathematical and computational models of translation have now been used for nearly five decades to investigate translation, and to shed light on the relationship between the different reactions in the system. This review gives an overview over the principal approaches used in the modelling efforts, and summarises some of the major findings that were made.
Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome.
Li, Xiaojun; Sun, Qingan; Jiang, Cai; Yang, Kailu; Hung, Li-Wei; Zhang, Junjie; Sacchettini, James C
2015-10-06
The ribosomal silencing factor RsfS slows cell growth by inhibiting protein synthesis during periods of diminished nutrient availability. The crystal structure of Mycobacterium tuberculosis (Mtb) RsfS, together with the cryo-electron microscopy (EM) structure of the large subunit 50S of Mtb ribosome, reveals how inhibition of protein synthesis by RsfS occurs. RsfS binds to the 50S at L14, which, when occupied, blocks the association of the small subunit 30S. Although Mtb RsfS is a dimer in solution, only a single subunit binds to 50S. The overlap between the dimer interface and the L14 binding interface confirms that the RsfS dimer must first dissociate to a monomer in order to bind to L14. RsfS interacts primarily through electrostatic and hydrogen bonding to L14. The EM structure shows extended rRNA density that it is not found in the Escherichia coli ribosome, the most striking of these being the extended RNA helix of H54a. Copyright © 2015 Elsevier Ltd. All rights reserved.
Implementation of Layered Decoding Architecture for LDPC Code using Layered Min-Sum Algorithm
Sandeep Kakde; Atish Khobragade; Shrikant Ambatkar; Pranay Nandanwar
2017-01-01
For binary field and long code lengths, Low Density Parity Check (LDPC) code approaches Shannon limit performance. LDPC codes provide remarkable error correction performance and therefore enlarge the design space for communication systems.In this paper, we have compare different digital modulation techniques and found that BPSK modulation technique is better than other modulation techniques in terms of BER. It also gives error performance of LDPC decoder over AWGN channel using Min-Sum algori...
Gongadze, G M
2011-12-01
5S rRNA is an integral component of the ribosome of all living organisms. It is known that the ribosome without 5S rRNA is functionally inactive. However, the question about the specific role of this RNA in functioning of the translation apparatus is still open. This review presents a brief history of the discovery of 5S rRNA and studies of its origin and localization in the ribosome. The previously expressed hypotheses about the role of this RNA in the functioning of the ribosome are discussed considering the unique location of 5S rRNA in the ribosome and its intermolecular contacts. Based on analysis of the current data on ribosome structure and its functional complexes, the role of 5S rRNA as an intermediary between ribosome functional domains is discussed.
Convolutional Encoder and Viterbi Decoder Using SOPC For Variable Constraint Length
DEFF Research Database (Denmark)
Kulkarni, Anuradha; Dnyaneshwar, Mantri; Prasad, Neeli R.
2013-01-01
Convolution encoder and Viterbi decoder are the basic and important blocks in any Code Division Multiple Accesses (CDMA). They are widely used in communication system due to their error correcting capability But the performance degrades with variable constraint length. In this context to have...... detailed analysis, this paper deals with the implementation of convolution encoder and Viterbi decoder using system on programming chip (SOPC). It uses variable constraint length of 7, 8 and 9 bits for 1/2 and 1/3 code rates. By analyzing the Viterbi algorithm it is seen that our algorithm has a better...
The fast decoding of Reed-Solomon codes using high-radix fermat theoretic transforms
Liu, K. Y.; Reed, I. S.; Truong, T. K.
1976-01-01
Fourier-like transforms over GF(F sub n), where F sub n = 2(2n) + 1 is a Fermat prime, are applied in decoding Reed-Solomon codes. It is shown that such transforms can be computed using high-radix fast Fourier transform (FFT) algorithms requiring considerably fewer multiplications than the more usual radix 2 FFT algorithm. A special 256-symbol, 16-symbol-error-correcting, Reed-Solomon (RS) code for space communication-link applications can be encoded and decoded using this high-radix FFT algorithm over GF(F sub 3).
Correcting quantum errors with entanglement.
Brun, Todd; Devetak, Igor; Hsieh, Min-Hsiu
2006-10-20
We show how entanglement shared between encoder and decoder can simplify the theory of quantum error correction. The entanglement-assisted quantum codes we describe do not require the dual-containing constraint necessary for standard quantum error-correcting codes, thus allowing us to "quantize" all of classical linear coding theory. In particular, efficient modern classical codes that attain the Shannon capacity can be made into entanglement-assisted quantum codes attaining the hashing bound (closely related to the quantum capacity). For systems without large amounts of shared entanglement, these codes can also be used as catalytic codes, in which a small amount of initial entanglement enables quantum communication.
"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.
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.
Jointly Decoded Raptor Codes: Analysis and Design for the BIAWGN Channel
Directory of Open Access Journals (Sweden)
Venkiah Auguste
2009-01-01
Full Text Available Abstract We are interested in the analysis and optimization of Raptor codes under a joint decoding framework, that is, when the precode and the fountain code exchange soft information iteratively. We develop an analytical asymptotic convergence analysis of the joint decoder, derive an optimization method for the design of efficient output degree distributions, and show that the new optimized distributions outperform the existing ones, both at long and moderate lengths. We also show that jointly decoded Raptor codes are robust to channel variation: they perform reasonably well over a wide range of channel capacities. This robustness property was already known for the erasure channel but not for the Gaussian channel. Finally, we discuss some finite length code design issues. Contrary to what is commonly believed, we show by simulations that using a relatively low rate for the precode , we can improve greatly the error floor performance of the Raptor code.
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
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...
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.
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.
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.
Control of ribosome formation in rat heart
International Nuclear Information System (INIS)
Russo, L.A.
1987-01-01
Diabetes of 9 days duration produced a 17% diminution in the rate of total protein synthesis in rat hearts perfused as Langendorff preparations supplied with glucose, plasma levels of amino acids, and 400 μU/ml insulin. This reduction was attributable to a decrease in efficiency of protein synthesis and total RNA content. Total messenger RNA content decreased in diabetic hearts in proportion to the reduction in total RNA. Diabetes also resulted in diminished ribosome content as reflected by the induction in total RNA. Ribosome production was investigated by monitoring incorporation of [ 3 H]phenylalanine into the proteins of cytoplasmic ribosomes. Rates of ribosome formation in diabetic hearts were as fast as control rates in the presence of insulin, and were faster than control rates in the absence of the hormone. These results indicated that ribosome content fell in diabetic hearts despite unchanged or faster rates of ribosome formation
Implementation of Layered Decoding Architecture for LDPC Code using Layered Min-Sum Algorithm
Directory of Open Access Journals (Sweden)
Sandeep Kakde
2017-12-01
Full Text Available For binary field and long code lengths, Low Density Parity Check (LDPC code approaches Shannon limit performance. LDPC codes provide remarkable error correction performance and therefore enlarge the design space for communication systems.In this paper, we have compare different digital modulation techniques and found that BPSK modulation technique is better than other modulation techniques in terms of BER. It also gives error performance of LDPC decoder over AWGN channel using Min-Sum algorithm. VLSI Architecture is proposed which uses the value re-use property of min-sum algorithm and gives high throughput. The proposed work has been implemented and tested on Xilinx Virtex 5 FPGA. The MATLAB result of LDPC decoder for low bit error rate (BER gives bit error rate in the range of 10-1 to 10-3.5 at SNR=1 to 2 for 20 no of iterations. So it gives good bit error rate performance. The latency of the parallel design of LDPC decoder has also reduced. It has accomplished 141.22 MHz maximum frequency and throughput of 2.02 Gbps while consuming less area of the design.
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 ...
tRNA's wobble decoding of the genome: 40 years of modification.
Agris, Paul F; Vendeix, Franck A P; Graham, William D
2007-02-09
The genetic code is degenerate, in that 20 amino acids are encoded by 61 triplet codes. In 1966, Francis Crick hypothesized that the cell's limited number of tRNAs decoded the genome by recognizing more than one codon. The ambiguity of that recognition resided in the third base-pair, giving rise to the Wobble Hypothesis. Post-transcriptional modifications at tRNA's wobble position 34, especially modifications of uridine 34, enable wobble to occur. The Modified Wobble Hypothesis proposed in 1991 that specific modifications of a tRNA wobble nucleoside shape the anticodon architecture in such a manner that interactions were restricted to the complementary base plus a single wobble pairing for amino acids with twofold degenerate codons. However, chemically different modifications at position 34 would expand the ability of a tRNA to read three or even four of the fourfold degenerate codons. One foundation of Crick's Wobble Hypothesis was that a near-constant geometry of canonical base-pairing be maintained in forming all three base-pairs between the tRNA anticodon and mRNA codon on the ribosome. In accepting an aminoacyl-tRNA, the ribosome requires maintenance of a specific geometry for the anticodon-codon base-pairing. However, it is the post-transcriptional modifications at tRNA wobble position 34 and purine 37, 3'-adjacent to the anticodon, that pre-structure the anticodon domain to ensure the correct codon binding. The modifications create both the architecture and the stability needed for decoding through restraints on anticodon stereochemistry and conformational space, and through selective hydrogen bonding. A physicochemical understanding of modified nucleoside contributions to the tRNA anticodon domain architecture and its decoding of the genome has advanced RNA world evolutionary theory, the principles of RNA chemistry, and the application of this knowledge to the introduction of new amino acids to proteins.
HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove.
Filbin, Megan E; Kieft, Jeffrey S
2011-07-01
Hepatitis C virus (HCV) uses a structured internal ribosome entry site (IRES) RNA to recruit the translation machinery to the viral RNA and begin protein synthesis without the ribosomal scanning process required for canonical translation initiation. Different IRES structural domains are used in this process, which begins with direct binding of the 40S ribosomal subunit to the IRES RNA and involves specific manipulation of the translational machinery. We have found that upon initial 40S subunit binding, the stem-loop domain of the IRES that contains the start codon unwinds and adopts a stable configuration within the subunit's decoding groove. This configuration depends on the sequence and structure of a different stem-loop domain (domain IIb) located far from the start codon in sequence, but spatially proximal in the IRES•40S complex. Mutation of domain IIb results in misconfiguration of the HCV RNA in the decoding groove that includes changes in the placement of the AUG start codon, and a substantial decrease in the ability of the IRES to initiate translation. Our results show that two distal regions of the IRES are structurally communicating at the initial step of 40S subunit binding and suggest that this is an important step in driving protein synthesis.
Saraiya, Ashesh A; Lamichhane, Tek N; Chow, Christine S; SantaLucia, John; Cunningham, Philip R
2008-02-22
The 970 loop (helix 31) of Escherichia coli 16S ribosomal RNA contains two modified nucleotides, m(2)G966 and m(5)C967. Positions A964, A969, and C970 are conserved among the Bacteria, Archaea, and Eukarya. The nucleotides present at positions 965, 966, 967, 968, and 971, however, are only conserved and unique within each domain. All organisms contain a modified nucleoside at position 966, but the type of the modification is domain specific. Biochemical and structure studies have placed this loop near the P site and have shown it to be involved in the decoding process and in binding the antibiotic tetracycline. To identify the functional components of this ribosomal RNA hairpin, the eight nucleotides of the 970 loop of helix 31 were subjected to saturation mutagenesis and 107 unique functional mutants were isolated and analyzed. Nonrandom nucleotide distributions were observed at each mutated position among the functional isolates. Nucleotide identity at positions 966 and 969 significantly affects ribosome function. Ribosomes with single mutations of m(2)G966 or m(5)C967 produce more protein in vivo than do wild-type ribosomes. Overexpression of initiation factor 3 specifically restored wild-type levels of protein synthesis to the 966 and 967 mutants, suggesting that modification of these residues is important for initiation factor 3 binding and for the proper initiation of protein synthesis.
Al-Hadid, Qais; White, Jonelle; Clarke, Steven
2016-02-12
A significant percentage of the methyltransferasome in Saccharomyces cerevisiae and higher eukaryotes is devoted to methylation of the translational machinery. Methylation of the RNA components of the translational machinery has been studied extensively and is important for structure stability, ribosome biogenesis, and translational fidelity. However, the functional effects of ribosomal protein methylation by their cognate methyltransferases are still largely unknown. Previous work has shown that the ribosomal protein Rpl3 methyltransferase, histidine protein methyltransferase 1 (Hpm1), is important for ribosome biogenesis and translation elongation fidelity. In this study, yeast strains deficient in each of the ten ribosomal protein methyltransferases in S. cerevisiae were examined for potential defects in ribosome biogenesis and translation. Like Hpm1-deficient cells, loss of four of the nine other ribosomal protein methyltransferases resulted in defects in ribosomal subunit synthesis. All of the mutant strains exhibited resistance to the ribosome inhibitors anisomycin and/or cycloheximide in plate assays, but not in liquid culture. Translational fidelity assays measuring stop codon readthrough, amino acid misincorporation, and programmed -1 ribosomal frameshifting, revealed that eight of the ten enzymes are important for translation elongation fidelity and the remaining two are necessary for translation termination efficiency. Altogether, these results demonstrate that ribosomal protein methyltransferases in S. cerevisiae play important roles in ribosome biogenesis and translation. Copyright © 2016 Elsevier Inc. All rights reserved.
Performance Analysis of CRC Codes for Systematic and Nonsystematic Polar Codes with List Decoding
Directory of Open Access Journals (Sweden)
Takumi Murata
2018-01-01
Full Text Available Successive cancellation list (SCL decoding of polar codes is an effective approach that can significantly outperform the original successive cancellation (SC decoding, provided that proper cyclic redundancy-check (CRC codes are employed at the stage of candidate selection. Previous studies on CRC-assisted polar codes mostly focus on improvement of the decoding algorithms as well as their implementation, and little attention has been paid to the CRC code structure itself. For the CRC-concatenated polar codes with CRC code as their outer code, the use of longer CRC code leads to reduction of information rate, whereas the use of shorter CRC code may reduce the error detection probability, thus degrading the frame error rate (FER performance. Therefore, CRC codes of proper length should be employed in order to optimize the FER performance for a given signal-to-noise ratio (SNR per information bit. In this paper, we investigate the effect of CRC codes on the FER performance of polar codes with list decoding in terms of the CRC code length as well as its generator polynomials. Both the original nonsystematic and systematic polar codes are considered, and we also demonstrate that different behaviors of CRC codes should be observed depending on whether the inner polar code is systematic or not.
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.
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.
Product code optimization for determinate state LDPC decoding in robust image transmission.
Thomos, Nikolaos; Boulgouris, Nikolaos V; Strintzis, Michael G
2006-08-01
We propose a novel scheme for error-resilient image transmission. The proposed scheme employs a product coder consisting of low-density parity check (LDPC) codes and Reed-Solomon codes in order to deal effectively with bit errors. The efficiency of the proposed scheme is based on the exploitation of determinate symbols in Tanner graph decoding of LDPC codes and a novel product code optimization technique based on error estimation. Experimental evaluation demonstrates the superiority of the proposed system in comparison to recent state-of-the-art techniques for image transmission.
Craciun, Stefan; Brockmeier, Austin J; George, Alan D; Lam, Herman; Príncipe, José C
2011-01-01
Methods for decoding movements from neural spike counts using adaptive filters often rely on minimizing the mean-squared error. However, for non-Gaussian distribution of errors, this approach is not optimal for performance. Therefore, rather than using probabilistic modeling, we propose an alternate non-parametric approach. In order to extract more structure from the input signal (neuronal spike counts) we propose using minimum error entropy (MEE), an information-theoretic approach that minimizes the error entropy as part of an iterative cost function. However, the disadvantage of using MEE as the cost function for adaptive filters is the increase in computational complexity. In this paper we present a comparison between the decoding performance of the analytic Wiener filter and a linear filter trained with MEE, which is then mapped to a parallel architecture in reconfigurable hardware tailored to the computational needs of the MEE filter. We observe considerable speedup from the hardware design. The adaptation of filter weights for the multiple-input, multiple-output linear filters, necessary in motor decoding, is a highly parallelizable algorithm. It can be decomposed into many independent computational blocks with a parallel architecture readily mapped to a field-programmable gate array (FPGA) and scales to large numbers of neurons. By pipelining and parallelizing independent computations in the algorithm, the proposed parallel architecture has sublinear increases in execution time with respect to both window size and filter order.
Trapping the ribosome to control gene expression.
Boehringer, Daniel; Ban, Nenad
2007-09-21
Protein synthesis is often regulated by structured mRNAs that interact with ribosomes. In this issue of Cell, Marzi et al. (2007) provide insights into the autoregulation of protein S15 by visualizing the folded repressor mRNA on the ribosome stalled in the preinitiation state. These results have implications for our understanding of the mechanism of translation initiation in general.
Differential Stoichiometry among Core Ribosomal Proteins
Directory of Open Access Journals (Sweden)
Nikolai Slavov
2015-11-01
Full Text Available Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its dysregulation in disease. While ribosomes are believed to have a fixed stoichiometry among their core ribosomal proteins (RPs, some experiments suggest a more variable composition. Testing such variability requires direct and precise quantification of RPs. We used mass spectrometry to directly quantify RPs across monosomes and polysomes of mouse embryonic stem cells (ESC and budding yeast. Our data show that the stoichiometry among core RPs in wild-type yeast cells and ESC depends both on the growth conditions and on the number of ribosomes bound per mRNA. Furthermore, we find that the fitness of cells with a deleted RP-gene is inversely proportional to the enrichment of the corresponding RP in polysomes. Together, our findings support the existence of ribosomes with distinct protein composition and physiological function.
In silico modelling and analysis of ribosome kinetics and aa-tRNA competition
Bošnački, D.; Pronk, T.E.; de Vink, E.P.
2008-01-01
We present a formal analysis of ribosome kinetics using probabilistic model checking and the tool Prism. We compute different parameters of the model, like probabilities of translation errors and average insertion times per codon. The model predicts strong correlation to the quotient of the
Iterative Decoding for an Optical CDMA based Laser communication System
International Nuclear Information System (INIS)
Kim, Jin Young; Kim, Eun Cheol; Cha, Jae Sang
2008-01-01
An optical CDMA(code division multiple access)based Laser communication system has attracted much attention since it requires minimal optical Laser signal processing and it is virtually delay free, while from the theoretical point of view, its performance depends on the auto and cross correlation properties of employed sequences. Various kinds of channel coding schemes for optical CDMA based Laser communication systems have been proposed and analyzed to compensate nonideal channel and receiver conditions in impaired photon channels. In this paper, we propose and analyze an iterative decoding of optical CDMA based Laser communication signals for both shot noise limited and thermal noise limited systems. It is assumed that optical channel is an intensity modulated (IM)channel and direct detection scheme is employed to detect the received optical signal. The performance is evaluated in terms of bit error probability and throughput. It is demonstrated that the BER and throughput performance is substantially improved with interleaver length for a fixed code rate and with alphabet size of PPM (pulse position modulation). Also, the BER and throughput performance is significantly enhanced with the number of iterations for decoding process. The results in this paper can be applied to the optical CDMA based Laser communication network with multiple access applications
Iterative Decoding for an Optical CDMA based Laser communication System
Energy Technology Data Exchange (ETDEWEB)
Kim, Jin Young; Kim, Eun Cheol [Kwangwoon Univ., Seoul (Korea, Republic of); Cha, Jae Sang [Seoul National Univ. of Technology, Seoul (Korea, Republic of)
2008-11-15
An optical CDMA(code division multiple access)based Laser communication system has attracted much attention since it requires minimal optical Laser signal processing and it is virtually delay free, while from the theoretical point of view, its performance depends on the auto and cross correlation properties of employed sequences. Various kinds of channel coding schemes for optical CDMA based Laser communication systems have been proposed and analyzed to compensate nonideal channel and receiver conditions in impaired photon channels. In this paper, we propose and analyze an iterative decoding of optical CDMA based Laser communication signals for both shot noise limited and thermal noise limited systems. It is assumed that optical channel is an intensity modulated (IM)channel and direct detection scheme is employed to detect the received optical signal. The performance is evaluated in terms of bit error probability and throughput. It is demonstrated that the BER and throughput performance is substantially improved with interleaver length for a fixed code rate and with alphabet size of PPM (pulse position modulation). Also, the BER and throughput performance is significantly enhanced with the number of iterations for decoding process. The results in this paper can be applied to the optical CDMA based Laser communication network with multiple access applications.
Decoding Problem Gamblers' Signals: A Decision Model for Casino Enterprises.
Ifrim, Sandra
2015-12-01
The aim of the present study is to offer a validated decision model for casino enterprises. The model enables those users to perform early detection of problem gamblers and fulfill their ethical duty of social cost minimization. To this end, the interpretation of casino customers' nonverbal communication is understood as a signal-processing problem. Indicators of problem gambling recommended by Delfabbro et al. (Identifying problem gamblers in gambling venues: final report, 2007) are combined with Viterbi algorithm into an interdisciplinary model that helps decoding signals emitted by casino customers. Model output consists of a historical path of mental states and cumulated social costs associated with a particular client. Groups of problem and non-problem gamblers were simulated to investigate the model's diagnostic capability and its cost minimization ability. Each group consisted of 26 subjects and was subsequently enlarged to 100 subjects. In approximately 95% of the cases, mental states were correctly decoded for problem gamblers. Statistical analysis using planned contrasts revealed that the model is relatively robust to the suppression of signals performed by casino clientele facing gambling problems as well as to misjudgments made by staff regarding the clients' mental states. Only if the last mentioned source of error occurs in a very pronounced manner, i.e. judgment is extremely faulty, cumulated social costs might be distorted.
Frame Decoder for Consultative Committee for Space Data Systems (CCSDS)
Reyes, Miguel A. De Jesus
2014-01-01
GNU Radio is a free and open source development toolkit that provides signal processing to implement software radios. It can be used with low-cost external RF hardware to create software defined radios, or without hardware in a simulation-like environment. GNU Radio applications are primarily written in Python and C++. The Universal Software Radio Peripheral (USRP) is a computer-hosted software radio designed by Ettus Research. The USRP connects to a host computer via high-speed Gigabit Ethernet. Using the open source Universal Hardware Driver (UHD), we can run GNU Radio applications using the USRP. An SDR is a "radio in which some or all physical layer functions are software defined"(IEEE Definition). A radio is any kind of device that wirelessly transmits or receives radio frequency (RF) signals in the radio frequency. An SDR is a radio communication system where components that have been typically implemented in hardware are implemented in software. GNU Radio has a generic packet decoder block that is not optimized for CCSDS frames. Using this generic packet decoder will add bytes to the CCSDS frames and will not permit for bit error correction using Reed-Solomon. The CCSDS frames consist of 256 bytes, including a 32-bit sync marker (0x1ACFFC1D). This frames are generated by the Space Data Processor and GNU Radio will perform the modulation and framing operations, including frame synchronization.
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.
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.
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.
Massey, J. L.
1976-01-01
Virtually all previously-suggested rate 1/2 binary convolutional codes with KE = 24 are compared. Their distance properties are given; and their performance, both in computation and in error probability, with sequential decoding on the deep-space channel is determined by simulation. Recommendations are made both for the choice of a specific KE = 24 code as well as for codes to be included in future coding standards for the deep-space channel. A new result given in this report is a method for determining the statistical significance of error probability data when the error probability is so small that it is not feasible to perform enough decoding simulations to obtain more than a very small number of decoding errors.
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.
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.
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
A Unified Approach to Restoration, Deinterlacing and Resolution Enhancement in Decoding MPEG-2 Video
DEFF Research Database (Denmark)
Forchhammer, Søren; Martins, Bo
2002-01-01
to the desired format. The processing involves an estimated quality of individual pixels based on MPEG image type and local quantization value. The mean-squared error (MSE) is reduced, compared to the directly decoded sequence, and annoying ringing artifacts, including mosquito noise, are effectively suppressed....... The superresolution pictures obtained by the algorithm are of much higher visual quality and have lower MSE than superresolution pictures obtained by simple spatial interpolation....
Error rate performance of narrowband multilevel CPFSK signals
Ekanayake, N.; Fonseka, K. J. P.
1987-04-01
The paper presents a relatively simple method for analyzing the effect of IF filtering on the performance of multilevel FM signals. Using this method, the error rate performance of narrowband FM signals is analyzed for three different detection techniques, namely limiter-discriminator detection, differential detection and coherent detection followed by differential decoding. The symbol error probabilities are computed for a Gaussian IF filter and a second-order Butterworth IF filter. It is shown that coherent detection and differential decoding yields better performance than limiter-discriminator detection and differential detection, whereas two noncoherent detectors yield approximately identical performance.
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.
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 ...
Probabilistic Amplitude Shaping With Hard Decision Decoding and Staircase Codes
Sheikh, Alireza; Amat, Alexandre Graell i.; Liva, Gianluigi; Steiner, Fabian
2018-05-01
We consider probabilistic amplitude shaping (PAS) as a means of increasing the spectral efficiency of fiber-optic communication systems. In contrast to previous works in the literature, we consider probabilistic shaping with hard decision decoding (HDD). In particular, we apply the PAS recently introduced by B\\"ocherer \\emph{et al.} to a coded modulation (CM) scheme with bit-wise HDD that uses a staircase code as the forward error correction code. We show that the CM scheme with PAS and staircase codes yields significant gains in spectral efficiency with respect to the baseline scheme using a staircase code and a standard constellation with uniformly distributed signal points. Using a single staircase code, the proposed scheme achieves performance within $0.57$--$1.44$ dB of the corresponding achievable information rate for a wide range of spectral efficiencies.
Coding and decoding for code division multiple user communication systems
Healy, T. J.
1985-01-01
A new algorithm is introduced which decodes code division multiple user communication signals. The algorithm makes use of the distinctive form or pattern of each signal to separate it from the composite signal created by the multiple users. Although the algorithm is presented in terms of frequency-hopped signals, the actual transmitter modulator can use any of the existing digital modulation techniques. The algorithm is applicable to error-free codes or to codes where controlled interference is permitted. It can be used when block synchronization is assumed, and in some cases when it is not. The paper also discusses briefly some of the codes which can be used in connection with the algorithm, and relates the algorithm to past studies which use other approaches to the same problem.
Exact performance analysis of decode-and-forward opportunistic relaying
Tourki, Kamel
2010-06-01
In this paper, we investigate a dual-hop decode-and-forward opportunistic relaying scheme where the source may or may not be able to communicate directly with the destination. In our study, we consider a regenerative relaying scheme in which the decision to cooperate takes into account the effect of the possible erroneously detected and transmitted data at the best relay. We derive an exact closed-form expression for the end-to-end bit-error rate (BER) of binary phase-shift keying (BPSK) modulation based on the exact statistics of each hop. Unlike existing works where the analysis focused on high signal-to-noise ratio (SNR) regime, such results are important to enable the designers to take decisions regarding practical systems that operate at low SNR regime. We show that performance simulation results coincide with our analytical results.
Selection combining for noncoherent decode-and-forward relay networks
Directory of Open Access Journals (Sweden)
Nguyen Ha
2011-01-01
Full Text Available Abstract This paper studies a new decode-and-forward relaying scheme for a cooperative wireless network composed of one source, K relays, and one destination and with binary frequency-shift keying modulation. A single threshold is employed to select retransmitting relays as follows: a relay retransmits to the destination if its decision variable is larger than the threshold; otherwise, it remains silent. The destination then performs selection combining for the detection of transmitted information. The average end-to-end bit-error-rate (BER is analytically determined in a closed-form expression. Based on the derived BER, the problem of choosing an optimal threshold or jointly optimal threshold and power allocation to minimize the end-to-end BER is also investigated. Both analytical and simulation results reveal that the obtained optimal threshold scheme or jointly optimal threshold and power-allocation scheme can significantly improve the BER performance compared to a previously proposed scheme.
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 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.
Oxidative damage of 18S and 5S ribosomal RNA in digestive gland of mussels exposed to trace metals.
Kournoutou, Georgia G; Giannopoulou, Panagiota C; Sazakli, Eleni; Leotsinidis, Michel; Kalpaxis, Dimitrios L
2017-11-01
Numerous studies have shown the ability of trace metals to accumulate in marine organisms and cause oxidative stress that leads to perturbations in many important intracellular processes, including protein synthesis. This study is mainly focused on the exploration of structural changes, like base modifications, scissions, and conformational changes, caused in 18S and 5S ribosomal RNA (rRNA) isolated from the mussel Mytilus galloprovincialis exposed to 40μg/L Cu, 30μg/L Hg, or 100μg/L Cd, for 5 or 15days. 18S rRNA and 5S rRNA are components of the small and large ribosomal subunit, respectively, found in complex with ribosomal proteins, translation factors and other auxiliary components (metal ions, toxins etc). 18S rRNA plays crucial roles in all stages of protein synthesis, while 5S rRNA serves as a master signal transducer between several functional regions of 28S rRNA. Therefore, structural changes in these ribosomal constituents could affect the basic functions of ribosomes and hence the normal metabolism of cells. Especially, 18S rRNA along with ribosomal proteins forms the decoding centre that ensures the correct codon-anticodon pairing. As exemplified by ELISA, primer extension analysis and DMS footprinting analysis, each metal caused oxidative damage to rRNA, depending on the nature of metal ion and the duration of exposure. Interestingly, exposure of mussels to Cu or Hg caused structural alterations in 5S rRNA, localized in paired regions and within loops A, B, C, and E, leading to a continuous progressive loss of the 5S RNA structural integrity. In contrast, structural impairments of 5S rRNA in mussels exposed to Cd were accumulating for the initial 5days, and then progressively decreased to almost the normal level by day 15, probably due to the parallel elevation of metallothionein content that depletes the pools of free Cd. Regions of interest in 18S rRNA, such as the decoding centre, sites implicated in the binding of tRNAs (A- and P-sites) or
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
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…
Cortical Decoding of Individual Finger and Wrist Kinematics for an Upper-Limb Neuroprosthesis
Aggarwal, Vikram; Tenore, Francesco; Acharya, Soumyadipta; Schieber, Marc H.; Thakor, Nitish V.
2010-01-01
Previous research has shown that neuronal activity can be used to continuously decode the kinematics of gross movements involving arm and hand trajectory. However, decoding the kinematics of fine motor movements, such as the manipulation of individual fingers, has not been demonstrated. In this study, single unit activities were recorded from task-related neurons in M1 of two trained rhesus monkey as they performed individuated movements of the fingers and wrist. The primates’ hand was placed in a manipulandum, and strain gauges at the tips of each finger were used to track the digit’s position. Both linear and non-linear filters were designed to simultaneously predict kinematics of each digit and the wrist, and their performance compared using mean squared error and correlation coefficients. All models had high decoding accuracy, but the feedforward ANN (R=0.76–0.86, MSE=0.04–0.05) and Kalman filter (R=0.68–0.86, MSE=0.04–0.07) performed better than a simple linear regression filter (0.58–0.81, 0.05–0.07). These results suggest that individual finger and wrist kinematics can be decoded with high accuracy, and be used to control a multi-fingered prosthetic hand in real-time. PMID:19964645
Population decoding of motor cortical activity using a generalized linear model with hidden states.
Lawhern, Vernon; Wu, Wei; Hatsopoulos, Nicholas; Paninski, Liam
2010-06-15
Generalized linear models (GLMs) have been developed for modeling and decoding population neuronal spiking activity in the motor cortex. These models provide reasonable characterizations between neural activity and motor behavior. However, they lack a description of movement-related terms which are not observed directly in these experiments, such as muscular activation, the subject's level of attention, and other internal or external states. Here we propose to include a multi-dimensional hidden state to address these states in a GLM framework where the spike count at each time is described as a function of the hand state (position, velocity, and acceleration), truncated spike history, and the hidden state. The model can be identified by an Expectation-Maximization algorithm. We tested this new method in two datasets where spikes were simultaneously recorded using a multi-electrode array in the primary motor cortex of two monkeys. It was found that this method significantly improves the model-fitting over the classical GLM, for hidden dimensions varying from 1 to 4. This method also provides more accurate decoding of hand state (reducing the mean square error by up to 29% in some cases), while retaining real-time computational efficiency. These improvements on representation and decoding over the classical GLM model suggest that this new approach could contribute as a useful tool to motor cortical decoding and prosthetic applications. Copyright (c) 2010 Elsevier B.V. All rights reserved.
Population Decoding of Motor Cortical Activity using a Generalized Linear Model with Hidden States
Lawhern, Vernon; Wu, Wei; Hatsopoulos, Nicholas G.; Paninski, Liam
2010-01-01
Generalized linear models (GLMs) have been developed for modeling and decoding population neuronal spiking activity in the motor cortex. These models provide reasonable characterizations between neural activity and motor behavior. However, they lack a description of movement-related terms which are not observed directly in these experiments, such as muscular activation, the subject's level of attention, and other internal or external states. Here we propose to include a multi-dimensional hidden state to address these states in a GLM framework where the spike count at each time is described as a function of the hand state (position, velocity, and acceleration), truncated spike history, and the hidden state. The model can be identified by an Expectation-Maximization algorithm. We tested this new method in two datasets where spikes were simultaneously recorded using a multi-electrode array in the primary motor cortex of two monkeys. It was found that this method significantly improves the model-fitting over the classical GLM, for hidden dimensions varying from 1 to 4. This method also provides more accurate decoding of hand state (lowering the Mean Square Error by up to 29% in some cases), while retaining real-time computational efficiency. These improvements on representation and decoding over the classical GLM model suggest that this new approach could contribute as a useful tool to motor cortical decoding and prosthetic applications. PMID:20359500
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu
2011-01-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We
Ribosome evolution: Emergence of peptide synthesis machinery
Indian Academy of Sciences (India)
suggested the dynamic movement of ribosomal proteins. The L2 protein (a .... Such kinds of interactions are important in elucidating the evolution of RNA .... Tamura K 2009 Molecular handedness of life: significance of RNA aminoacylation.
Is The Ribosome Targeted By Adaptive Mutations
DEFF Research Database (Denmark)
Jimenez Fernandez, Alicia; Molin, Søren; Johansen, Helle Krogh
2015-01-01
Introduction: RNA polymerase and ribosomes, composing the macromolecular synthesis machinery (MMSM), carry out the central processes of transcription and translation, but are usually seen as mechanical elements with no regulatory function. Extensive investigations of gene regulation and the high ...
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....
DEFF Research Database (Denmark)
Grankowski, N; Gasior, E; Issinger, O G
1993-01-01
Kinetic studies on the 60S protein kinase were conducted with synthetic peptides and ribosomal proteins as substrate. Peptide RRREEESDDD proved to be the best synthetic substrate for this enzyme. The peptide has a sequence of amino acids which most closely resembles the structure of potential...... phosphorylation sites in natural substrates, i.e., acidic ribosomal proteins. The superiority of certain kinetic parameters for 60S kinase obtained with the native whole 80S ribosomes over those of the isolated fraction of acidic ribosomal proteins indicates that the affinity of 60S kinase to the specific protein...
Crystallization of ribosomes from Thermus thermophilus
International Nuclear Information System (INIS)
Karpova, E.A.; Serdyuk, I.N.; Tarkhovskii, Yu.S.; Orlova, E.V.; Borovyagin, V.L.
1987-01-01
An understanding of the molecular bases of the process of protein biosynthesis on the ribosome requires a knowledge of its structure with high three-dimensional resolution involving the method of x-ray crystallographic analysis. The authors report on the production of crystals of the 70S ribosomes from a new source - the highly thermophilic bacterium Thermus thermophilus. Ribosomes for crystallization were obtained from Th. thermophilus strain HB8 by two washings in buffer with high ionic strength. The ribosome preparation was investigated for homogeneity by the method of high-speed sedimentation in a buffer containing 15 mM MgCl 2 , 50 mM NH 4 Cl, and 10 MM Tris-HCl, pH 7.5. Analysis showed that the preparation if homogeneous. The same preparation was investigated for intactness of ribosomal RNA by the method of gel electrophoresis in 2.75% acrylamide 0.5% agarose gel in a buffer containing 30 mM Tris, 30 mM NaH 2 PO 4 , 10 mM EDTA, 1-2% SDS, and 6 M urea. Analysis showed that the preparation possesses intact 16S and 23S RNA. The latter did not degrade, at least in a week of exposure of the ribosomes in buffer solution at 5 0 C. The ribosome preparation had no appreciable RNase activity, which was verified by incubating 4.5 micrograms of ribosomes with 3 micrograms of 14 C-labeled 16S rRna (50 0 C, 90 min) in a buffer containing 10 mM MgCl 2 , 100 mM NH 4 Cl, and 10 mM Tris-HCl, pH/sub 20 0 / 7.5. The incubated nonhydrolyzed RNA was precipitated with 5% trichloroacetic acid and applied on a GF/C filter. The radioactivity was determined in a toluene scintillator on an LS-100C counter
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.
Faster 2-regular information-set decoding
Bernstein, D.J.; Lange, T.; Peters, C.P.; Schwabe, P.; Chee, Y.M.
2011-01-01
Fix positive integers B and w. Let C be a linear code over F 2 of length Bw. The 2-regular-decoding problem is to find a nonzero codeword consisting of w length-B blocks, each of which has Hamming weight 0 or 2. This problem appears in attacks on the FSB (fast syndrome-based) hash function and
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.
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
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...
Older Adults Have Difficulty in Decoding Sarcasm
Phillips, Louise H.; Allen, Roy; Bull, Rebecca; Hering, Alexandra; Kliegel, Matthias; Channon, Shelley
2015-01-01
Younger and older adults differ in performance on a range of social-cognitive skills, with older adults having difficulties in decoding nonverbal cues to emotion and intentions. Such skills are likely to be important when deciding whether someone is being sarcastic. In the current study we investigated in a life span sample whether there are…
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.
Triple-Error-Correcting Codec ASIC
Jones, Robert E.; Segallis, Greg P.; Boyd, Robert
1994-01-01
Coder/decoder constructed on single integrated-circuit chip. Handles data in variety of formats at rates up to 300 Mbps, correcting up to 3 errors per data block of 256 to 512 bits. Helps reduce cost of transmitting data. Useful in many high-data-rate, bandwidth-limited communication systems such as; personal communication networks, cellular telephone networks, satellite communication systems, high-speed computing networks, broadcasting, and high-reliability data-communication links.
Error floor behavior study of LDPC codes for concatenated codes design
Chen, Weigang; Yin, Liuguo; Lu, Jianhua
2007-11-01
Error floor behavior of low-density parity-check (LDPC) codes using quantized decoding algorithms is statistically studied with experimental results on a hardware evaluation platform. The results present the distribution of the residual errors after decoding failure and reveal that the number of residual error bits in a codeword is usually very small using quantized sum-product (SP) algorithm. Therefore, LDPC code may serve as the inner code in a concatenated coding system with a high code rate outer code and thus an ultra low error floor can be achieved. This conclusion is also verified by the experimental results.
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)
Lee, L.-N.
1977-01-01
Concatenated coding systems utilizing a convolutional code as the inner code and a Reed-Solomon code as the outer code are considered. In order to obtain very reliable communications over a very noisy channel with relatively modest coding complexity, it is proposed to concatenate a byte-oriented unit-memory convolutional code with an RS outer code whose symbol size is one byte. It is further proposed to utilize a real-time minimal-byte-error probability decoding algorithm, together with feedback from the outer decoder, in the decoder for the inner convolutional code. The performance of the proposed concatenated coding system is studied, and the improvement over conventional concatenated systems due to each additional feature is isolated.
Machine-learning-assisted correction of correlated qubit errors in a topological code
Directory of Open Access Journals (Sweden)
Paul Baireuther
2018-01-01
Full Text Available A fault-tolerant quantum computation requires an efficient means to detect and correct errors that accumulate in encoded quantum information. In the context of machine learning, neural networks are a promising new approach to quantum error correction. Here we show that a recurrent neural network can be trained, using only experimentally accessible data, to detect errors in a widely used topological code, the surface code, with a performance above that of the established minimum-weight perfect matching (or blossom decoder. The performance gain is achieved because the neural network decoder can detect correlations between bit-flip (X and phase-flip (Z errors. The machine learning algorithm adapts to the physical system, hence no noise model is needed. The long short-term memory layers of the recurrent neural network maintain their performance over a large number of quantum error correction cycles, making it a practical decoder for forthcoming experimental realizations of the surface code.
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.
Directory of Open Access Journals (Sweden)
Rachmad Vidya Wicaksana Putra
2016-06-01
Full Text Available Convolutional encoding and data decoding are fundamental processes in convolutional error correction. One of the most popular error correction methods in decoding is the Viterbi algorithm. It is extensively implemented in many digital communication applications. Its VLSI design challenges are about area, speed, power, complexity and configurability. In this research, we specifically propose a VLSI architecture for a configurable and low-complexity design of a hard-decision Viterbi decoding algorithm. The configurable and low-complexity design is achieved by designing a generic VLSI architecture, optimizing each processing element (PE at the logical operation level and designing a conditional adapter. The proposed design can be configured for any predefined number of trace-backs, only by changing the trace-back parameter value. Its computational process only needs N + 2 clock cycles latency, with N is the number of trace-backs. Its configurability function has been proven for N = 8, N = 16, N = 32 and N = 64. Furthermore, the proposed design was synthesized and evaluated in Xilinx and Altera FPGA target boards for area consumption and speed performance.
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.
Ribosomal studies on the 70S ribosome of E.coli by means of neutron scattering
International Nuclear Information System (INIS)
Burkhardt, N.
1997-01-01
Ribosomes are ribonucleo-protein complexes, which catalyse proteinbiosynthesis in all living organisms. Currently, most of the structural models of the prokaryotic 70S ribosome rely on electron microscopy and describe mainly the outer shape of the particle. Neutron scattering can provide information on the internal structure of the ribosome. Parts of the structure can be contrasted for neutrons by means of an isotopic exchange of the naturally occurring hydrogen ( 1 H) for deuterium ( 2 H), allowing direct measurements in situ. Specifically deuterium-labeled ribosomes (E. coli) were prepared and analysed with neutron scattering. The biochemical methods were established and combined to a generally applicable preparation system. This allows labeling of all ribosomal components in any combination. A systematic analysis of the protein and RNA phases resulted in the development of a new model for the 70S ribosome. This model describes not only the outer shape of the particle, but displays also an experimentally determined internal protein-RNA distribution and the border of subunits for the first time (four-phase model; resolution: 50A). Models of the 70S ribosome from other studies were evaluated and ranked according to consistency with the measured scattering data. Applying a new neutron scattering technique of particular sensitivity, the proton-spin contrast-variation, single proteins could be measured and localized. The positions of the proteins S6 and S10 were determined, providing the first coordinates of protein mass centers within the 70S ribosome. (orig.) [de
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
Joint Carrier-Phase Synchronization and LDPC Decoding
Simon, Marvin; Valles, Esteban
2009-01-01
A method has been proposed to increase the degree of synchronization of a radio receiver with the phase of a suppressed carrier signal modulated with a binary- phase-shift-keying (BPSK) or quaternary- phase-shift-keying (QPSK) signal representing a low-density parity-check (LDPC) code. This method is an extended version of the method described in Using LDPC Code Constraints to Aid Recovery of Symbol Timing (NPO-43112), NASA Tech Briefs, Vol. 32, No. 10 (October 2008), page 54. Both methods and the receiver architectures in which they would be implemented belong to a class of timing- recovery methods and corresponding receiver architectures characterized as pilotless in that they do not require transmission and reception of pilot signals. The proposed method calls for the use of what is known in the art as soft decision feedback to remove the modulation from a replica of the incoming signal prior to feeding this replica to a phase-locked loop (PLL) or other carrier-tracking stage in the receiver. Soft decision feedback refers to suitably processed versions of intermediate results of iterative computations involved in the LDPC decoding process. Unlike a related prior method in which hard decision feedback (the final sequence of decoded symbols) is used to remove the modulation, the proposed method does not require estimation of the decoder error probability. In a basic digital implementation of the proposed method, the incoming signal (having carrier phase theta theta (sub c) plus noise would first be converted to inphase (I) and quadrature (Q) baseband signals by mixing it with I and Q signals at the carrier frequency [wc/(2 pi)] generated by a local oscillator. The resulting demodulated signals would be processed through one-symbol-period integrate and- dump filters, the outputs of which would be sampled and held, then multiplied by a soft-decision version of the baseband modulated signal. The resulting I and Q products consist of terms proportional to the cosine
International Nuclear Information System (INIS)
Knuefer; Lindauer
1980-01-01
Besides that at spectacular events a combination of component failure and human error is often found. Especially the Rasmussen-Report and the German Risk Assessment Study show for pressurised water reactors that human error must not be underestimated. Although operator errors as a form of human error can never be eliminated entirely, they can be minimized and their effects kept within acceptable limits if a thorough training of personnel is combined with an adequate design of the plant against accidents. Contrary to the investigation of engineering errors, the investigation of human errors has so far been carried out with relatively small budgets. Intensified investigations in this field appear to be a worthwhile effort. (orig.)
Error Resilient Video Compression Using Behavior Models
Directory of Open Access Journals (Sweden)
Jacco R. Taal
2004-03-01
Full Text Available Wireless and Internet video applications are inherently subjected to bit errors and packet errors, respectively. This is especially so if constraints on the end-to-end compression and transmission latencies are imposed. Therefore, it is necessary to develop methods to optimize the video compression parameters and the rate allocation of these applications that take into account residual channel bit errors. In this paper, we study the behavior of a predictive (interframe video encoder and model the encoders behavior using only the statistics of the original input data and of the underlying channel prone to bit errors. The resulting data-driven behavior models are then used to carry out group-of-pictures partitioning and to control the rate of the video encoder in such a way that the overall quality of the decoded video with compression and channel errors is optimized.
Energy Technology Data Exchange (ETDEWEB)
Loughry, Thomas A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2015-02-01
As the volume of data acquired by space-based sensors increases, mission data compression/decompression and forward error correction code processing performance must likewise scale. This competency development effort was explored using the General Purpose Graphics Processing Unit (GPGPU) to accomplish high-rate Rice Decompression and high-rate Reed-Solomon (RS) decoding at the satellite mission ground station. Each algorithm was implemented and benchmarked on a single GPGPU. Distributed processing across one to four GPGPUs was also investigated. The results show that the GPGPU has considerable potential for performing satellite communication Data Signal Processing, with three times or better performance improvements and up to ten times reduction in cost over custom hardware, at least in the case of Rice Decompression and Reed-Solomon Decoding.
Decoding Different Patterns in Various Grey Tones Incorporated in the QR Code
Directory of Open Access Journals (Sweden)
Filip Cvitić
2014-07-01
Full Text Available Using colors in bar codes causes errors that may adversely affect their readability (Tan etal. 2010, given that the contrast between data and background modules is reduced. Due to the unreliability of using color bar codes, most designers still keep to the limitations placed by Pira International (Smithers Pira in 2002 (Williams, 2004. Since the contrast between data modules and background modules is the most important aspect in the process of reliable bar code decoding, this paper explores the dependence of reliable decoding of QR codes incorporated with combinations of grey tones on the technical characteristics of the cameras on smartphones that were marketed in the period between 2008 and 2012.
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%.
Directory of Open Access Journals (Sweden)
Bani Kumar Pathak
Full Text Available BACKGROUND: Molecular chaperones that support de novo folding of proteins under non stress condition are classified as chaperone 'foldases' that are distinct from chaperone' holdases' that provide high affinity binding platform for unfolded proteins and prevent their aggregation specifically under stress conditions. Ribosome, the cellular protein synthesis machine can act as a foldase chaperone that can bind unfolded proteins and release them in folding competent state. The peptidyl transferase center (PTC located in the domain V of the 23S rRNA of Escherichia coli ribosome (bDV RNA is the chaperoning center of the ribosome. It has been proposed that via specific interactions between the RNA and refolding proteins, the chaperone provides information for the correct folding of unfolded polypeptide chains. RESULTS: We demonstrate using Escherichia coli ribosome and variants of its domain V RNA that the ribosome can bind to partially folded intermediates of bovine carbonic anhydrase II (BCAII and lysozyme and suppress aggregation during their refolding. Using mutants of domain V RNA we demonstrate that the time for which the chaperone retains the bound protein is an important factor in determining its ability to suppress aggregation and/or support reactivation of protein. CONCLUSION: The ribosome can behave like a 'holdase' chaperone and has the ability to bind and hold back partially folded intermediate states of proteins from participating in the aggregation process. Since the ribosome is an essential organelle that is present in large numbers in all living cells, this ability of the ribosome provides an energetically inexpensive way to suppress cellular aggregation. Further, this ability of the ribosome might also be crucial in the context that the ribosome is one of the first chaperones to be encountered by a large nascent polypeptide chains that have a tendency to form partially folded intermediates immediately following their synthesis.
Logical error rate scaling of the toric code
International Nuclear Information System (INIS)
Watson, Fern H E; Barrett, Sean D
2014-01-01
To date, a great deal of attention has focused on characterizing the performance of quantum error correcting codes via their thresholds, the maximum correctable physical error rate for a given noise model and decoding strategy. Practical quantum computers will necessarily operate below these thresholds meaning that other performance indicators become important. In this work we consider the scaling of the logical error rate of the toric code and demonstrate how, in turn, this may be used to calculate a key performance indicator. We use a perfect matching decoding algorithm to find the scaling of the logical error rate and find two distinct operating regimes. The first regime admits a universal scaling analysis due to a mapping to a statistical physics model. The second regime characterizes the behaviour in the limit of small physical error rate and can be understood by counting the error configurations leading to the failure of the decoder. We present a conjecture for the ranges of validity of these two regimes and use them to quantify the overhead—the total number of physical qubits required to perform error correction. (paper)
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
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.
Xiong, Chenrong; Yan, Zhiyuan
2014-10-01
Non-binary low-density parity-check (LDPC) codes have some advantages over their binary counterparts, but unfortunately their decoding complexity is a significant challenge. The iterative hard- and soft-reliability based majority-logic decoding algorithms are attractive for non-binary LDPC codes, since they involve only finite field additions and multiplications as well as integer operations and hence have significantly lower complexity than other algorithms. In this paper, we propose two improvements to the majority-logic decoding algorithms. Instead of the accumulation of reliability information in the existing majority-logic decoding algorithms, our first improvement is a new reliability information update. The new update not only results in better error performance and fewer iterations on average, but also further reduces computational complexity. Since existing majority-logic decoding algorithms tend to have a high error floor for codes whose parity check matrices have low column weights, our second improvement is a re-selection scheme, which leads to much lower error floors, at the expense of more finite field operations and integer operations, by identifying periodic points, re-selecting intermediate hard decisions, and changing reliability information.
Can Emotional and Behavioral Dysregulation in Youth Be Decoded from Functional Neuroimaging?
Directory of Open Access Journals (Sweden)
Liana C L Portugal
Full Text Available High comorbidity among pediatric disorders characterized by behavioral and emotional dysregulation poses problems for diagnosis and treatment, and suggests that these disorders may be better conceptualized as dimensions of abnormal behaviors. Furthermore, identifying neuroimaging biomarkers related to dimensional measures of behavior may provide targets to guide individualized treatment. We aimed to use functional neuroimaging and pattern regression techniques to determine whether patterns of brain activity could accurately decode individual-level severity on a dimensional scale measuring behavioural and emotional dysregulation at two different time points.A sample of fifty-seven youth (mean age: 14.5 years; 32 males was selected from a multi-site study of youth with parent-reported behavioral and emotional dysregulation. Participants performed a block-design reward paradigm during functional Magnetic Resonance Imaging (fMRI. Pattern regression analyses consisted of Relevance Vector Regression (RVR and two cross-validation strategies implemented in the Pattern Recognition for Neuroimaging toolbox (PRoNTo. Medication was treated as a binary confounding variable. Decoded and actual clinical scores were compared using Pearson's correlation coefficient (r and mean squared error (MSE to evaluate the models. Permutation test was applied to estimate significance levels.Relevance Vector Regression identified patterns of neural activity associated with symptoms of behavioral and emotional dysregulation at the initial study screen and close to the fMRI scanning session. The correlation and the mean squared error between actual and decoded symptoms were significant at the initial study screen and close to the fMRI scanning session. However, after controlling for potential medication effects, results remained significant only for decoding symptoms at the initial study screen. Neural regions with the highest contribution to the pattern regression model
Lonardi, Stefano; Mirebrahim, Hamid; Wanamaker, Steve; Alpert, Matthew; Ciardo, Gianfranco; Duma, Denisa; Close, Timothy J
2015-09-15
As the invention of DNA sequencing in the 70s, computational biologists have had to deal with the problem of de novo genome assembly with limited (or insufficient) depth of sequencing. In this work, we investigate the opposite problem, that is, the challenge of dealing with excessive depth of sequencing. We explore the effect of ultra-deep sequencing data in two domains: (i) the problem of decoding reads to bacterial artificial chromosome (BAC) clones (in the context of the combinatorial pooling design we have recently proposed), and (ii) the problem of de novo assembly of BAC clones. Using real ultra-deep sequencing data, we show that when the depth of sequencing increases over a certain threshold, sequencing errors make these two problems harder and harder (instead of easier, as one would expect with error-free data), and as a consequence the quality of the solution degrades with more and more data. For the first problem, we propose an effective solution based on 'divide and conquer': we 'slice' a large dataset into smaller samples of optimal size, decode each slice independently, and then merge the results. Experimental results on over 15 000 barley BACs and over 4000 cowpea BACs demonstrate a significant improvement in the quality of the decoding and the final assembly. For the second problem, we show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencing data. Python scripts to process slices and resolve decoding conflicts are available from http://goo.gl/YXgdHT; software Hashfilter can be downloaded from http://goo.gl/MIyZHs stelo@cs.ucr.edu or timothy.close@ucr.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Instanton-based techniques for analysis and reduction of error floors of LDPC codes
International Nuclear Information System (INIS)
Chertkov, Michael; Chilappagari, Shashi K.; Stepanov, Mikhail G.; Vasic, Bane
2008-01-01
We describe a family of instanton-based optimization methods developed recently for the analysis of the error floors of low-density parity-check (LDPC) codes. Instantons are the most probable configurations of the channel noise which result in decoding failures. We show that the general idea and the respective optimization technique are applicable broadly to a variety of channels, discrete or continuous, and variety of sub-optimal decoders. Specifically, we consider: iterative belief propagation (BP) decoders, Gallager type decoders, and linear programming (LP) decoders performing over the additive white Gaussian noise channel (AWGNC) and the binary symmetric channel (BSC). The instanton analysis suggests that the underlying topological structures of the most probable instanton of the same code but different channels and decoders are related to each other. Armed with this understanding of the graphical structure of the instanton and its relation to the decoding failures, we suggest a method to construct codes whose Tanner graphs are free of these structures, and thus have less significant error floors.
Instanton-based techniques for analysis and reduction of error floor of LDPC codes
Energy Technology Data Exchange (ETDEWEB)
Chertkov, Michael [Los Alamos National Laboratory; Chilappagari, Shashi K [Los Alamos National Laboratory; Stepanov, Mikhail G [Los Alamos National Laboratory; Vasic, Bane [SENIOR MEMBER, IEEE
2008-01-01
We describe a family of instanton-based optimization methods developed recently for the analysis of the error floors of low-density parity-check (LDPC) codes. Instantons are the most probable configurations of the channel noise which result in decoding failures. We show that the general idea and the respective optimization technique are applicable broadly to a variety of channels, discrete or continuous, and variety of sub-optimal decoders. Specifically, we consider: iterative belief propagation (BP) decoders, Gallager type decoders, and linear programming (LP) decoders performing over the additive white Gaussian noise channel (AWGNC) and the binary symmetric channel (BSC). The instanton analysis suggests that the underlying topological structures of the most probable instanton of the same code but different channels and decoders are related to each other. Armed with this understanding of the graphical structure of the instanton and its relation to the decoding failures, we suggest a method to construct codes whose Tanner graphs are free of these structures, and thus have less significant error floors.
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...
Decoding divergent series in nonparaxial optics.
Borghi, Riccardo; Gori, Franco; Guattari, Giorgio; Santarsiero, Massimo
2011-03-15
A theoretical analysis aimed at investigating the divergent character of perturbative series involved in the study of free-space nonparaxial propagation of vectorial optical beams is proposed. Our analysis predicts a factorial divergence for such series and provides a theoretical framework within which the results of recently published numerical experiments concerning nonparaxial propagation of vectorial Gaussian beams find a meaningful interpretation in terms of the decoding operated on such series by the Weniger transformation.
Directory of Open Access Journals (Sweden)
Nicolai Lang, Hans Peter Büchler
2018-01-01
Full Text Available Active quantum error correction on topological codes is one of the most promising routes to long-term qubit storage. In view of future applications, the scalability of the used decoding algorithms in physical implementations is crucial. In this work, we focus on the one-dimensional Majorana chain and construct a strictly local decoder based on a self-dual cellular automaton. We study numerically and analytically its performance and exploit these results to contrive a scalable decoder with exponentially growing decoherence times in the presence of noise. Our results pave the way for scalable and modular designs of actively corrected one-dimensional topological quantum memories.
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.
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
Huang, Shijie; Zhu, Xuechen; Melançon, Charles E
2016-01-15
The ribosome is the quintessential antibacterial drug target, with many structurally and mechanistically distinct classes of antibacterial agents acting by inhibiting ribosome function. Detecting and quantifying ribosome inhibition by small molecules and investigating their binding modes and mechanisms of action are critical to antibacterial drug discovery and development efforts. To develop a ribosome inhibition assay that is operationally simple, yet provides direct information on the drug target and the mechanism of action, we have developed engineered E. coli strains harboring an orthogonal ribosome-controlled green fluorescent protein (GFP) reporter that produce fluorescent signal when the orthogonal ribosome is inhibited. As a proof of concept, we demonstrate that these strains, when coexpressing homogeneous populations of aminoglycoside resistant ribosomes, act as sensitive and quantitative detectors of ribosome inhibition by a set of 12 structurally diverse aminoglycoside antibiotics. We suggest that this strategy can be extended to quantifying ribosome inhibition by other drug classes.
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.
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.
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
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
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.
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....
International Nuclear Information System (INIS)
Winterflood, A.H.
1980-01-01
In discussing Einstein's Special Relativity theory it is claimed that it violates the principle of relativity itself and that an anomalous sign in the mathematics is found in the factor which transforms one inertial observer's measurements into those of another inertial observer. The apparent source of this error is discussed. Having corrected the error a new theory, called Observational Kinematics, is introduced to replace Einstein's Special Relativity. (U.K.)
Effect of primary and secondary radicals on chain breaks in ribosomal RNA in E. coli ribosomes
International Nuclear Information System (INIS)
Singh, H.; Bishop, J.
1984-01-01
It has been shown previously that, in dilute aerated solutions, ribosomes are inactivated by OH radicals and by secondary radicals produced from added alcohols (Singh and Vadasz 1983 a). In de-aerated solutions, both radicalH and e - sub(aq) also inactivate ribosomes (Singh and Vadasz 1983 b). The results of these studies and other on different systems (Adams et al. 1973, Aldrich and Cundall 1969, Dewey and Stein 1970, Masuda et al. 1971, Nabben et al. 1982, 1983, Samuni et al. 1980, Singh and Singh 1982) have shown that damage to biological systems occurs by diverse mechanisms. One of these mechanisms involves chain breaks in RNA (Pollard and Weller 1967). The purpose of this study was to determine which of the primary and secondary radicals cause chain breaks in ribosomal RNA (rRNA) within the ribosomes. (author)
Analysis of error-correction constraints in an optical disk
Roberts, Jonathan D.; Ryley, Alan; Jones, David M.; Burke, David
1996-07-01
The compact disk read-only memory (CD-ROM) is a mature storage medium with complex error control. It comprises four levels of Reed Solomon codes allied to a sequence of sophisticated interleaving strategies and 8:14 modulation coding. New storage media are being developed and introduced that place still further demands on signal processing for error correction. It is therefore appropriate to explore thoroughly the limit of existing strategies to assess future requirements. We describe a simulation of all stages of the CD-ROM coding, modulation, and decoding. The results of decoding the burst error of a prescribed number of modulation bits are discussed in detail. Measures of residual uncorrected error within a sector are displayed by C1, C2, P, and Q error counts and by the status of the final cyclic redundancy check (CRC). Where each data sector is encoded separately, it is shown that error-correction performance against burst errors depends critically on the position of the burst within a sector. The C1 error measures the burst length, whereas C2 errors reflect the burst position. The performance of Reed Solomon product codes is shown by the P and Q statistics. It is shown that synchronization loss is critical near the limits of error correction. An example is given of miscorrection that is identified by the CRC check.
Memory-efficient decoding of LDPC codes
Kwok-San Lee, Jason; Thorpe, Jeremy; Hawkins, Jon
2005-01-01
We present a low-complexity quantization scheme for the implementation of regular (3,6) LDPC codes. The quantization parameters are optimized to maximize the mutual information between the source and the quantized messages. Using this non-uniform quantized belief propagation algorithm, we have simulated that an optimized 3-bit quantizer operates with 0.2dB implementation loss relative to a floating point decoder, and an optimized 4-bit quantizer operates less than 0.1dB quantization loss.
[Modulation of Metacognition with Decoded Neurofeedback].
Koizumi, Ai; Cortese, Aurelio; Amano, Kaoru; Kawato, Mitsuo; Lau, Hakwan
2017-12-01
Humans often assess their confidence in their own perception, e.g., feeling "confident" or "certain" of having seen a friend, or feeling "uncertain" about whether the phone rang. The neural mechanism underlying the metacognitive function that reflects subjective perception still remains under debate. We have previously used decoded neurofeedback (DecNef) to demonstrate that manipulating the multivoxel activation patterns in the frontoparietal network modulates perceptual confidence without affecting perceptual performance. The results provided clear evidence for a dissociation between perceptual confidence and performance and suggested a distinct role of the frontoparietal network in metacognition.
Maximum a posteriori decoder for digital communications
Altes, Richard A. (Inventor)
1997-01-01
A system and method for decoding by identification of the most likely phase coded signal corresponding to received data. The present invention has particular application to communication with signals that experience spurious random phase perturbations. The generalized estimator-correlator uses a maximum a posteriori (MAP) estimator to generate phase estimates for correlation with incoming data samples and for correlation with mean phases indicative of unique hypothesized signals. The result is a MAP likelihood statistic for each hypothesized transmission, wherein the highest value statistic identifies the transmitted signal.
Photonic entanglement-assisted quantum low-density parity-check encoders and decoders.
Djordjevic, Ivan B
2010-05-01
I propose encoder and decoder architectures for entanglement-assisted (EA) quantum low-density parity-check (LDPC) codes suitable for all-optical implementation. I show that two basic gates needed for EA quantum error correction, namely, controlled-NOT (CNOT) and Hadamard gates can be implemented based on Mach-Zehnder interferometer. In addition, I show that EA quantum LDPC codes from balanced incomplete block designs of unitary index require only one entanglement qubit to be shared between source and destination.
Threshold Multi Split-Row algorithm for decoding irregular LDPC codes
Directory of Open Access Journals (Sweden)
Chakir Aqil
2017-12-01
Full Text Available In this work, we propose a new threshold multi split-row algorithm in order to improve the multi split-row algorithm for LDPC irregular codes decoding. We give a complete description of our algorithm as well as its advantages for the LDPC codes. The simulation results over an additive white gaussian channel show that an improvement in code error performance between 0.4 dB and 0.6 dB compared to the multi split-row algorithm.
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,
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…
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)
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…
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
GTPases and the origin of the ribosome
Directory of Open Access Journals (Sweden)
Smith Temple F
2010-05-01
Full Text Available Abstract Background This paper is an attempt to trace the evolution of the ribosome through the evolution of the universal P-loop GTPases that are involved with the ribosome in translation and with the attachment of the ribosome to the membrane. The GTPases involved in translation in Bacteria/Archaea are the elongation factors EFTu/EF1, the initiation factors IF2/aeIF5b + aeIF2, and the elongation factors EFG/EF2. All of these GTPases also contain the OB fold also found in the non GTPase IF1 involved in initiation. The GTPase involved in the signal recognition particle in most Bacteria and Archaea is SRP54. Results 1 The Elongation Factors of the Archaea based on structural considerations of the domains have the following evolutionary path: EF1→ aeIF2 → EF2. The evolution of the aeIF5b was a later event; 2 the Elongation Factors of the Bacteria based on the topological considerations of the GTPase domain have a similar evolutionary path: EFTu→ IF→2→EFG. These evolutionary sequences reflect the evolution of the LSU followed by the SSU to form the ribosome; 3 the OB-fold IF1 is a mimic of an ancient tRNA minihelix. Conclusion The evolution of translational GTPases of both the Archaea and Bacteria point to the evolution of the ribosome. The elongation factors, EFTu/EF1, began as a Ras-like GTPase bringing the activated minihelix tRNA to the Large Subunit Unit. The initiation factors and elongation factor would then have evolved from the EFTu/EF1 as the small subunit was added to the evolving ribosome. The SRP has an SRP54 GTPase and a specific RNA fold in its RNA component similar to the PTC. We consider the SRP to be a remnant of an ancient form of an LSU bound to a membrane. Reviewers This article was reviewed by George Fox, Leonid Mirny and Chris Sander.
Decoding magnetoencephalographic rhythmic activity using spectrospatial information.
Kauppi, Jukka-Pekka; Parkkonen, Lauri; Hari, Riitta; Hyvärinen, Aapo
2013-12-01
We propose a new data-driven decoding method called Spectral Linear Discriminant Analysis (Spectral LDA) for the analysis of magnetoencephalography (MEG). The method allows investigation of changes in rhythmic neural activity as a result of different stimuli and tasks. The introduced classification model only assumes that each "brain state" can be characterized as a combination of neural sources, each of which shows rhythmic activity at one or several frequency bands. Furthermore, the model allows the oscillation frequencies to be different for each such state. We present decoding results from 9 subjects in a four-category classification problem defined by an experiment involving randomly alternating epochs of auditory, visual and tactile stimuli interspersed with rest periods. The performance of Spectral LDA was very competitive compared with four alternative classifiers based on different assumptions concerning the organization of rhythmic brain activity. In addition, the spectral and spatial patterns extracted automatically on the basis of trained classifiers showed that Spectral LDA offers a novel and interesting way of analyzing spectrospatial oscillatory neural activity across the brain. All the presented classification methods and visualization tools are freely available as a Matlab toolbox. © 2013.
Unsupervised learning of facial emotion decoding skills
Directory of Open Access Journals (Sweden)
Jan Oliver Huelle
2014-02-01
Full Text Available Research on the mechanisms underlying human facial emotion recognition has long focussed on genetically determined neural algorithms and often neglected the question of how these algorithms might be tuned by social learning. Here we show that facial emotion decoding skills can be significantly and sustainably improved by practise without an external teaching signal. Participants saw video clips of dynamic facial expressions of five different women and were asked to decide which of four possible emotions (anger, disgust, fear and sadness was shown in each clip. Although no external information about the correctness of the participant’s response or the sender’s true affective state was provided, participants showed a significant increase of facial emotion recognition accuracy both within and across two training sessions two days to several weeks apart. We discuss several similarities and differences between the unsupervised improvement of facial decoding skills observed in the current study, unsupervised perceptual learning of simple stimuli described in previous studies and practise effects often observed in cognitive tasks.
Unsupervised learning of facial emotion decoding skills.
Huelle, Jan O; Sack, Benjamin; Broer, Katja; Komlewa, Irina; Anders, Silke
2014-01-01
Research on the mechanisms underlying human facial emotion recognition has long focussed on genetically determined neural algorithms and often neglected the question of how these algorithms might be tuned by social learning. Here we show that facial emotion decoding skills can be significantly and sustainably improved by practice without an external teaching signal. Participants saw video clips of dynamic facial expressions of five different women and were asked to decide which of four possible emotions (anger, disgust, fear, and sadness) was shown in each clip. Although no external information about the correctness of the participant's response or the sender's true affective state was provided, participants showed a significant increase of facial emotion recognition accuracy both within and across two training sessions two days to several weeks apart. We discuss several similarities and differences between the unsupervised improvement of facial decoding skills observed in the current study, unsupervised perceptual learning of simple stimuli described in previous studies and practice effects often observed in cognitive tasks.
Bayer image parallel decoding based on GPU
Hu, Rihui; Xu, Zhiyong; Wei, Yuxing; Sun, Shaohua
2012-11-01
In the photoelectrical tracking system, Bayer image is decompressed in traditional method, which is CPU-based. However, it is too slow when the images become large, for example, 2K×2K×16bit. In order to accelerate the Bayer image decoding, this paper introduces a parallel speedup method for NVIDA's Graphics Processor Unit (GPU) which supports CUDA architecture. The decoding procedure can be divided into three parts: the first is serial part, the second is task-parallelism part, and the last is data-parallelism part including inverse quantization, inverse discrete wavelet transform (IDWT) as well as image post-processing part. For reducing the execution time, the task-parallelism part is optimized by OpenMP techniques. The data-parallelism part could advance its efficiency through executing on the GPU as CUDA parallel program. The optimization techniques include instruction optimization, shared memory access optimization, the access memory coalesced optimization and texture memory optimization. In particular, it can significantly speed up the IDWT by rewriting the 2D (Tow-dimensional) serial IDWT into 1D parallel IDWT. Through experimenting with 1K×1K×16bit Bayer image, data-parallelism part is 10 more times faster than CPU-based implementation. Finally, a CPU+GPU heterogeneous decompression system was designed. The experimental result shows that it could achieve 3 to 5 times speed increase compared to the CPU serial method.
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,…
Directory of Open Access Journals (Sweden)
T. Kalavathi Devi
2015-01-01
Full Text Available Convolutional codes are comprehensively used as Forward Error Correction (FEC codes in digital communication systems. For decoding of convolutional codes at the receiver end, Viterbi decoder is often used to have high priority. This decoder meets the demand of high speed and low power. At present, the design of a competent system in Very Large Scale Integration (VLSI technology requires these VLSI parameters to be finely defined. The proposed asynchronous method focuses on reducing the power consumption of Viterbi decoder for various constraint lengths using asynchronous modules. The asynchronous designs are based on commonly used Quasi Delay Insensitive (QDI templates, namely, Precharge Half Buffer (PCHB and Weak Conditioned Half Buffer (WCHB. The functionality of the proposed asynchronous design is simulated and verified using Tanner Spice (TSPICE in 0.25 µm, 65 nm, and 180 nm technologies of Taiwan Semiconductor Manufacture Company (TSMC. The simulation result illustrates that the asynchronous design techniques have 25.21% of power reduction compared to synchronous design and work at a speed of 475 MHz.
Implementasi Encoder dan Decoder Cyclic Redundancy Check Pada TMS320C6416T
Directory of Open Access Journals (Sweden)
Grace Natalia
2014-03-01
Full Text Available CRC merupakan metode yang paling populer digunakan saat ini karena kemampuanya paling baik dalam mendeteksi error. Pada Tugas Akhir ini memaparkan bagaimana CRC diimplementasikan pada TMS320C6416T. Evaluasi yang akan diteliti yaitu kinerja proses encoder dan decoder CRC sebagai fungsi Eb/No dari error per blok melalui kanal ideal AWGN dengan modulasi BPSK serta melihat seberapa besar kemampuan CRC dalam mendeteksi kesalahan. Pengujian yang dilakukan melalui simulink matlab dan implementasi secara real ke dalam TMS320C6416T. Adapun kode CRC yang dipilih yaitu CRC-8 dan CRC-16 dimana pada implementasi pada TMS dilakukan pengiriman sebesar 100.000 bit dalam 12.500 frame. Hasil pengujian yang diperoleh yaitu jumlah error yang dideteksi pada CRC-8 rata-rata jumlah error adalah 2.750 frame dan rata-rata jumlah error bit informasi 1.957 bit. Sedangkan untuk CRC-16 rata-rata jumlah error adalah 3.520 frame dan rata-rata jumlah error per bit informasi yaitu 1.971 bit. Dari pengujian membuktikan bahwa kemampuan CRC-16 dalam menjaga keamanan data bit informasi jauh lebih baik dibandingkan dengan CRC-8.
Fuchs, Gabriele; Petrov, Alexey N; Marceau, Caleb D; Popov, Lauren M; Chen, Jin; O'Leary, Seán E; Wang, Richard; Carette, Jan E; Sarnow, Peter; Puglisi, Joseph D
2015-01-13
Translation initiation can occur by multiple pathways. To delineate these pathways by single-molecule methods, fluorescently labeled ribosomal subunits are required. Here, we labeled human 40S ribosomal subunits with a fluorescent SNAP-tag at ribosomal protein eS25 (RPS25). The resulting ribosomal subunits could be specifically labeled in living cells and in vitro. Using single-molecule Förster resonance energy transfer (FRET) between RPS25 and domain II of the hepatitis C virus (HCV) internal ribosome entry site (IRES), we measured the rates of 40S subunit arrival to the HCV IRES. Our data support a single-step model of HCV IRES recruitment to 40S subunits, irreversible on the initiation time scale. We furthermore demonstrated that after binding, the 40S:HCV IRES complex is conformationally dynamic, undergoing slow large-scale rearrangements. Addition of translation extracts suppresses these fluctuations, funneling the complex into a single conformation on the 80S assembly pathway. These findings show that 40S:HCV IRES complex formation is accompanied by dynamic conformational rearrangements that may be modulated by initiation factors.
The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
Bieri, Philipp; Leibundgut, Marc; Saurer, Martin; Boehringer, Daniel; Ban, Nenad
2017-02-15
Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.
The "periodic table" of the genetic code: A new way to look at the code and the decoding process.
Komar, Anton A
2016-01-01
Henri Grosjean and Eric Westhof recently presented an information-rich, alternative view of the genetic code, which takes into account current knowledge of the decoding process, including the complex nature of interactions between mRNA, tRNA and rRNA that take place during protein synthesis on the ribosome, and it also better reflects the evolution of the code. The new asymmetrical circular genetic code has a number of advantages over the traditional codon table and the previous circular diagrams (with a symmetrical/clockwise arrangement of the U, C, A, G bases). Most importantly, all sequence co-variances can be visualized and explained based on the internal logic of the thermodynamics of codon-anticodon interactions.
Constrained motion estimation-based error resilient coding for HEVC
Guo, Weihan; Zhang, Yongfei; Li, Bo
2018-04-01
Unreliable communication channels might lead to packet losses and bit errors in the videos transmitted through it, which will cause severe video quality degradation. This is even worse for HEVC since more advanced and powerful motion estimation methods are introduced to further remove the inter-frame dependency and thus improve the coding efficiency. Once a Motion Vector (MV) is lost or corrupted, it will cause distortion in the decoded frame. More importantly, due to motion compensation, the error will propagate along the motion prediction path, accumulate over time, and significantly degrade the overall video presentation quality. To address this problem, we study the problem of encoder-sider error resilient coding for HEVC and propose a constrained motion estimation scheme to mitigate the problem of error propagation to subsequent frames. The approach is achieved by cutting off MV dependencies and limiting the block regions which are predicted by temporal motion vector. The experimental results show that the proposed method can effectively suppress the error propagation caused by bit errors of motion vector and can improve the robustness of the stream in the bit error channels. When the bit error probability is 10-5, an increase of the decoded video quality (PSNR) by up to1.310dB and on average 0.762 dB can be achieved, compared to the reference HEVC.
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.
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.
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.
Ribosomal history reveals origins of modern protein synthesis.
Directory of Open Access Journals (Sweden)
Ajith Harish
Full Text Available The origin and evolution of the ribosome is central to our understanding of the cellular world. Most hypotheses posit that the ribosome originated in the peptidyl transferase center of the large ribosomal subunit. However, these proposals do not link protein synthesis to RNA recognition and do not use a phylogenetic comparative framework to study ribosomal evolution. Here we infer evolution of the structural components of the ribosome. Phylogenetic methods widely used in morphometrics are applied directly to RNA structures of thousands of molecules and to a census of protein structures in hundreds of genomes. We find that components of the small subunit involved in ribosomal processivity evolved earlier than the catalytic peptidyl transferase center responsible for protein synthesis. Remarkably, subunit RNA and proteins coevolved, starting with interactions between the oldest proteins (S12 and S17 and the oldest substructure (the ribosomal ratchet in the small subunit and ending with the rise of a modern multi-subunit ribosome. Ancestral ribonucleoprotein components show similarities to in vitro evolved RNA replicase ribozymes and protein structures in extant replication machinery. Our study therefore provides important clues about the chicken-or-egg dilemma associated with the central dogma of molecular biology by showing that ribosomal history is driven by the gradual structural accretion of protein and RNA structures. Most importantly, results suggest that functionally important and conserved regions of the ribosome were recruited and could be relics of an ancient ribonucleoprotein world.
Li, Yue (Inventor); Bruck, Jehoshua (Inventor)
2018-01-01
A data device includes a memory having a plurality of memory cells configured to store data values in accordance with a predetermined rank modulation scheme that is optional and a memory controller that receives a current error count from an error decoder of the data device for one or more data operations of the flash memory device and selects an operating mode for data scrubbing in accordance with the received error count and a program cycles count.
Decoding emotional valence from electroencephalographic rhythmic activity.
Celikkanat, Hande; Moriya, Hiroki; Ogawa, Takeshi; Kauppi, Jukka-Pekka; Kawanabe, Motoaki; Hyvarinen, Aapo
2017-07-01
We attempt to decode emotional valence from electroencephalographic rhythmic activity in a naturalistic setting. We employ a data-driven method developed in a previous study, Spectral Linear Discriminant Analysis, to discover the relationships between the classification task and independent neuronal sources, optimally utilizing multiple frequency bands. A detailed investigation of the classifier provides insight into the neuronal sources related with emotional valence, and the individual differences of the subjects in processing emotions. Our findings show: (1) sources whose locations are similar across subjects are consistently involved in emotional responses, with the involvement of parietal sources being especially significant, and (2) even though the locations of the involved neuronal sources are consistent, subjects can display highly varying degrees of valence-related EEG activity in the sources.
Decoding the mechanisms of Antikythera astronomical device
Lin, Jian-Liang
2016-01-01
This book presents a systematic design methodology for decoding the interior structure of the Antikythera mechanism, an astronomical device from ancient Greece. The historical background, surviving evidence and reconstructions of the mechanism are introduced, and the historical development of astronomical achievements and various astronomical instruments are investigated. Pursuing an approach based on the conceptual design of modern mechanisms and bearing in mind the standards of science and technology at the time, all feasible designs of the six lost/incomplete/unclear subsystems are synthesized as illustrated examples, and 48 feasible designs of the complete interior structure are presented. This approach provides not only a logical tool for applying modern mechanical engineering knowledge to the reconstruction of the Antikythera mechanism, but also an innovative research direction for identifying the original structures of the mechanism in the future. In short, the book offers valuable new insights for all...
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...
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...
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
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....
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
Encoding and Decoding Models in Cognitive Electrophysiology
Directory of Open Access Journals (Sweden)
Christopher R. Holdgraf
2017-09-01
Full Text Available Cognitive neuroscience has seen rapid growth in the size and complexity of data recorded from the human brain as well as in the computational tools available to analyze this data. This data explosion has resulted in an increased use of multivariate, model-based methods for asking neuroscience questions, allowing scientists to investigate multiple hypotheses with a single dataset, to use complex, time-varying stimuli, and to study the human brain under more naturalistic conditions. These tools come in the form of “Encoding” models, in which stimulus features are used to model brain activity, and “Decoding” models, in which neural features are used to generated a stimulus output. Here we review the current state of encoding and decoding models in cognitive electrophysiology and provide a practical guide toward conducting experiments and analyses in this emerging field. Our examples focus on using linear models in the study of human language and audition. We show how to calculate auditory receptive fields from natural sounds as well as how to decode neural recordings to predict speech. The paper aims to be a useful tutorial to these approaches, and a practical introduction to using machine learning and applied statistics to build models of neural activity. The data analytic approaches we discuss may also be applied to other sensory modalities, motor systems, and cognitive systems, and we cover some examples in these areas. In addition, a collection of Jupyter notebooks is publicly available as a complement to the material covered in this paper, providing code examples and tutorials for predictive modeling in python. The aim is to provide a practical understanding of predictive modeling of human brain data and to propose best-practices in conducting these analyses.
DEFF Research Database (Denmark)
Issinger, O G
1977-01-01
Two acidic proteins from 80-S ribosomes were isolated and purified to homogeneity. The purified acidic proteins could be phosphorylated by casein kinase using [gamma-32P]ATP and [gamma-32P]GTP as a phosphoryl donor. The proteins became phosphorylated in situ, too. Sodium dodecyl sulfate polyacryl......Two acidic proteins from 80-S ribosomes were isolated and purified to homogeneity. The purified acidic proteins could be phosphorylated by casein kinase using [gamma-32P]ATP and [gamma-32P]GTP as a phosphoryl donor. The proteins became phosphorylated in situ, too. Sodium dodecyl sulfate...
Brain-to-text: Decoding spoken phrases from phone representations in the brain
Directory of Open Access Journals (Sweden)
Christian eHerff
2015-06-01
Full Text Available It has long been speculated whether communication between humans and machines based on natural speech related cortical activity is possible. Over the past decade, studies have suggested that it is feasible to recognize isolated aspects of speech from neural signals, such as auditory features, phones or one of a few isolated words. However, until now it remained an unsolved challenge to decode continuously spoken speech from the neural substrate associated with speech and language processing. Here, we show for the first time that continuously spoken speech can be decoded into the expressed words from intracranial electrocorticographic (ECoG recordings. Specifically, we implemented a system, which we call Brain-To-Text that models single phones, employs techniques from automatic speech recognition (ASR, and thereby transforms brain activity while speaking into the corresponding textual representation. Our results demonstrate that our system achieved word error rates as low as 25% and phone error rates below 50%. Additionally, our approach contributes to the current understanding of the neural basis of continuous speech production by identifying those cortical regions that hold substantial information about individual phones. In conclusion, the Brain-To-Text system described in this paper represents an important step towards human-machine communication based on imagined speech.
Directory of Open Access Journals (Sweden)
Monique N O'Leary
Full Text Available Most yeast ribosomal protein genes are duplicated and their characterization has led to hypotheses regarding the existence of specialized ribosomes with different subunit composition or specifically-tailored functions. In yeast, ribosomal protein genes are generally duplicated and evidence has emerged that paralogs might have specific roles. Unlike yeast, most mammalian ribosomal proteins are thought to be encoded by a single gene copy, raising the possibility that heterogenous populations of ribosomes are unique to yeast. Here, we examine the roles of the mammalian Rpl22, finding that Rpl22(-/- mice have only subtle phenotypes with no significant translation defects. We find that in the Rpl22(-/- mouse there is a compensatory increase in Rpl22-like1 (Rpl22l1 expression and incorporation into ribosomes. Consistent with the hypothesis that either ribosomal protein can support translation, knockdown of Rpl22l1 impairs growth of cells lacking Rpl22. Mechanistically, Rpl22 regulates Rpl22l1 directly by binding to an internal hairpin structure and repressing its expression. We propose that ribosome specificity may exist in mammals, providing evidence that one ribosomal protein can influence composition of the ribosome by regulating its own paralog.
Architecture of the large subunit of the mammalian mitochondrial ribosome.
Greber, Basil J; Boehringer, Daniel; Leitner, Alexander; Bieri, Philipp; Voigts-Hoffmann, Felix; Erzberger, Jan P; Leibundgut, Marc; Aebersold, Ruedi; Ban, Nenad
2014-01-23
Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by oxidative phosphorylation. The ribosomes in mammalian mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins. Here we present the three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution. The structure, combined with data from chemical crosslinking and mass spectrometry experiments, reveals the unique features of the 39S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site. This region of the mitochondrial ribosome has been considerably remodelled compared to its bacterial counterpart, providing a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain.
FPGA implementation of high-performance QC-LDPC decoder for optical communications
Zou, Ding; Djordjevic, Ivan B.
2015-01-01
Forward error correction is as one of the key technologies enabling the next-generation high-speed fiber optical communications. Quasi-cyclic (QC) low-density parity-check (LDPC) codes have been considered as one of the promising candidates due to their large coding gain performance and low implementation complexity. In this paper, we present our designed QC-LDPC code with girth 10 and 25% overhead based on pairwise balanced design. By FPGAbased emulation, we demonstrate that the 5-bit soft-decision LDPC decoder can achieve 11.8dB net coding gain with no error floor at BER of 10-15 avoiding using any outer code or post-processing method. We believe that the proposed single QC-LDPC code is a promising solution for 400Gb/s optical communication systems and beyond.
Percolation bounds for decoding thresholds with correlated erasures in quantum LDPC codes
Hamilton, Kathleen; Pryadko, Leonid
Correlations between errors can dramatically affect decoding thresholds, in some cases eliminating the threshold altogether. We analyze the existence of a threshold for quantum low-density parity-check (LDPC) codes in the case of correlated erasures. When erasures are positively correlated, the corresponding multi-variate Bernoulli distribution can be modeled in terms of cluster errors, where qubits in clusters of various size can be marked all at once. In a code family with distance scaling as a power law of the code length, erasures can be always corrected below percolation on a qubit adjacency graph associated with the code. We bound this correlated percolation transition by weighted (uncorrelated) percolation on a specially constructed cluster connectivity graph, and apply our recent results to construct several bounds for the latter. This research was supported in part by the NSF Grant PHY-1416578 and by the ARO Grant W911NF-14-1-0272.
Placeholder factors in ribosome biogenesis: please, pave my way
Directory of Open Access Journals (Sweden)
Francisco J. Espinar-Marchena
2017-04-01
Full Text Available The synthesis of cytoplasmic eukaryotic ribosomes is an extraordinarily energy-demanding cellular activity that occurs progressively from the nucleolus to the cytoplasm. In the nucleolus, precursor rRNAs associate with a myriad of trans-acting factors and some ribosomal proteins to form pre-ribosomal particles. These factors include snoRNPs, nucleases, ATPases, GTPases, RNA helicases, and a vast list of proteins with no predicted enzymatic activity. Their coordinate activity orchestrates in a spatiotemporal manner the modification and processing of precursor rRNAs, the rearrangement reactions required for the formation of productive RNA folding intermediates, the ordered assembly of the ribosomal proteins, and the export of pre-ribosomal particles to the cytoplasm; thus, providing speed, directionality and accuracy to the overall process of formation of translation-competent ribosomes. Here, we review a particular class of trans-acting factors known as “placeholders”. Placeholder factors temporarily bind selected ribosomal sites until these have achieved a structural context that is appropriate for exchanging the placeholder with another site-specific binding factor. By this strategy, placeholders sterically prevent premature recruitment of subsequently binding factors, premature formation of structures, avoid possible folding traps, and act as molecular clocks that supervise the correct progression of pre-ribosomal particles into functional ribosomal subunits. We summarize the current understanding of those factors that delay the assembly of distinct ribosomal proteins or subsequently bind key sites in pre-ribosomal particles. We also discuss recurrent examples of RNA-protein and protein-protein mimicry between rRNAs and/or factors, which have clear functional implications for the ribosome biogenesis pathway.
The architecture of mammalian ribosomal protein promoters
Directory of Open Access Journals (Sweden)
Perry Robert P
2005-02-01
Full Text Available Abstract Background Mammalian ribosomes contain 79 different proteins encoded by widely scattered single copy genes. Coordinate expression of these genes at transcriptional and post-transcriptional levels is required to ensure a roughly equimolar accumulation of ribosomal proteins. To date, detailed studies of only a very few ribosomal protein (rp promoters have been made. To elucidate the general features of rp promoter architecture, I made a detailed sequence comparison of the promoter regions of the entire set of orthologous human and mouse rp genes. Results A striking evolutionarily conserved feature of most rp genes is the separation by an intron of the sequences involved in transcriptional and translational regulation from the sequences with protein encoding function. Another conserved feature is the polypyrimidine initiator, which conforms to the consensus (Y2C+1TY(T2(Y3. At least 60 % of the rp promoters contain a largely conserved TATA box or A/T-rich motif, which should theoretically have TBP-binding capability. A remarkably high proportion of the promoters contain conserved binding sites for transcription factors that were previously implicated in rp gene expression, namely upstream GABP and Sp1 sites and downstream YY1 sites. Over 80 % of human and mouse rp genes contain a transposable element residue within 900 bp of 5' flanking sequence; very little sequence identity between human and mouse orthologues was evident more than 200 bp upstream of the transcriptional start point. Conclusions This analysis has provided some valuable insights into the general architecture of mammalian rp promoters and has identified parameters that might coordinately regulate the transcriptional activity of certain subsets of rp genes.
Molecular dynamics simulation of ribosome jam
Matsumoto, Shigenori
2011-09-01
We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.
Ribosomal RNA: a key to phylogeny
Olsen, G. J.; Woese, C. R.
1993-01-01
As molecular phylogeny increasingly shapes our understanding of organismal relationships, no molecule has been applied to more questions than have ribosomal RNAs. We review this role of the rRNAs and some of the insights that have been gained from them. We also offer some of the practical considerations in extracting the phylogenetic information from the sequences. Finally, we stress the importance of comparing results from multiple molecules, both as a method for testing the overall reliability of the organismal phylogeny and as a method for more broadly exploring the history of the genome.
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...
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.
Illustrative examples in a bilingual decoding dictionary: An (un ...
African Journals Online (AJOL)
Keywords: Illustrative Examples, Bilingual Decoding Dictionary, Semantic Differences Between Source Language (Sl) And Target Language (Tl), Grammatical Differences Between Sl And Tl, Translation Of Examples, Transposition, Context-Dependent Translation, One-Word Equivalent, Zero Equivalent, Idiomatic ...
Decoding Reed-Solomon Codes beyond half the minimum distance
DEFF Research Database (Denmark)
Høholdt, Tom; Nielsen, Rasmus Refslund
1999-01-01
We describe an efficient implementation of M.Sudan"s algorithm for decoding Reed-Solomon codes beyond half the minimum distance. Furthermore we calculate an upper bound of the probabilty of getting more than one codeword as output...
Eukaryotic ribosome display with in situ DNA recovery.
He, Mingyue; Edwards, Bryan M; Kastelic, Damjana; Taussig, Michael J
2012-01-01
Ribosome display is a cell-free display technology for in vitro selection and optimisation of proteins from large diversified libraries. It operates through the formation of stable protein-ribosome-mRNA (PRM) complexes and selection of ligand-binding proteins, followed by DNA recovery from the selected genetic information. Both prokaryotic and eukaryotic ribosome display systems have been developed. In this chapter, we describe the eukaryotic rabbit reticulocyte method in which a distinct in situ single-primer RT-PCR procedure is used to recover DNA from the selected PRM complexes without the need for prior disruption of the ribosome.
Huang, Jen-Fa; Yang, Chao-Chin; Tseng, Shin-Pin
2004-01-01
In this paper, an optical code-division multiple-access (OCDMA) system with complementary Walsh-Hadamard coded optical encoder/decoder configuration structured over arrayed-waveguide grating (AWG) routers is examined. In the proposed system, each network user requires only two AWG routers to accomplish spectral encoding and decoding for complementary keying, thus, resulting a simpler and low cost system. Performance of the proposed system is analyzed by taking the effect of phase-induced intensity noise into account. The result indicates that the established system not only preserves the capability of suppressing multiple-access interference (MAI), but also improves bit-error-rate performance as compared to the conventional coders employing simple on-off keying.
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 ...
In Profile: Models of Ribosome Biogenesis Defects and Regulation of Protein Synthesis
Essers, P.B.M.
2013-01-01
Ribosomes are the mediators of protein synthesis in the cell and therefore crucial to proper cell function. In addition, ribosomes are highly abundant, with ribosomal RNA making up 80% of the RNA in the cell. A large amount of resources go into maintaining this pool of ribosomes, so ribosome
Vinay BC; Nikhitha MK; Patel Sunil B
2015-01-01
In this present review article, regarding medication errors its definition, medication error problem, types of medication errors, common causes of medication errors, monitoring medication errors, consequences of medication errors, prevention of medication error and managing medication errors have been explained neatly and legibly with proper tables which is easy to understand.
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.
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.
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.
Directory of Open Access Journals (Sweden)
Brittany Burton
Full Text Available Assembly of the ribosome from its protein and RNA constituents has been studied extensively over the past 50 years, and experimental evidence suggests that prokaryotic ribosomal proteins undergo conformational changes during assembly. However, to date, no studies have attempted to elucidate these conformational changes. The present work utilizes computational methods to analyze protein dynamics and to investigate the linkage between dynamics and binding of these proteins during the assembly of the ribosome. Ribosomal proteins are known to be positively charged and we find the percentage of positive residues in r-proteins to be about twice that of the average protein: Lys+Arg is 18.7% for E. coli and 21.2% for T. thermophilus. Also, positive residues constitute a large proportion of RNA contacting residues: 39% for E. coli and 46% for T. thermophilus. This affirms the known importance of charge-charge interactions in the assembly of the ribosome. We studied the dynamics of three primary proteins from E. coli and T. thermophilus 30S subunits that bind early in the assembly (S15, S17, and S20 with atomic molecular dynamic simulations, followed by a study of all r-proteins using elastic network models. Molecular dynamics simulations show that solvent-exposed proteins (S15 and S17 tend to adopt more stable solution conformations than an RNA-embedded protein (S20. We also find protein residues that contact the 16S rRNA are generally more mobile in comparison with the other residues. This is because there is a larger proportion of contacting residues located in flexible loop regions. By the use of elastic network models, which are computationally more efficient, we show that this trend holds for most of the 30S r-proteins.
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.
Defining the bacteroides ribosomal binding site.
Wegmann, Udo; Horn, Nikki; Carding, Simon R
2013-03-01
The human gastrointestinal tract, in particular the colon, hosts a vast number of commensal microorganisms. Representatives of the genus Bacteroides are among the most abundant bacterial species in the human colon. Bacteroidetes diverged from the common line of eubacterial descent before other eubacterial groups. As a result, they employ unique transcription initiation signals and, because of this uniqueness, they require specific genetic tools. Although some tools exist, they are not optimal for studying the roles and functions of these bacteria in the human gastrointestinal tract. Focusing on translation initiation signals in Bacteroides, we created a series of expression vectors allowing for different levels of protein expression in this genus, and we describe the use of pepI from Lactobacillus delbrueckii subsp. lactis as a novel reporter gene for Bacteroides. Furthermore, we report the identification of the 3' end of the 16S rRNA of Bacteroides ovatus and analyze in detail its ribosomal binding site, thus defining a core region necessary for efficient translation, which we have incorporated into the design of our expression vectors. Based on the sequence logo information from the 5' untranslated region of other Bacteroidales ribosomal protein genes, we conclude that our findings are relevant to all members of this order.
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.
Kim, HyungGoo R.; Pitkow, Xaq; Angelaki, Dora E.
2016-01-01
Sensory input reflects events that occur in the environment, but multiple events may be confounded in sensory signals. For example, under many natural viewing conditions, retinal image motion reflects some combination of self-motion and movement of objects in the world. To estimate one stimulus event and ignore others, the brain can perform marginalization operations, but the neural bases of these operations are poorly understood. Using computational modeling, we examine how multisensory signals may be processed to estimate the direction of self-motion (i.e., heading) and to marginalize out effects of object motion. Multisensory neurons represent heading based on both visual and vestibular inputs and come in two basic types: “congruent” and “opposite” cells. Congruent cells have matched heading tuning for visual and vestibular cues and have been linked to perceptual benefits of cue integration during heading discrimination. Opposite cells have mismatched visual and vestibular heading preferences and are ill-suited for cue integration. We show that decoding a mixed population of congruent and opposite cells substantially reduces errors in heading estimation caused by object motion. In addition, we present a general formulation of an optimal linear decoding scheme that approximates marginalization and can be implemented biologically by simple reinforcement learning mechanisms. We also show that neural response correlations induced by task-irrelevant variables may greatly exceed intrinsic noise correlations. Overall, our findings suggest a general computational strategy by which neurons with mismatched tuning for two different sensory cues may be decoded to perform marginalization operations that dissociate possible causes of sensory inputs. PMID:27334948
Optical RAM row access using WDM-enabled all-passive row/column decoders
Papaioannou, Sotirios; Alexoudi, Theoni; Kanellos, George T.; Miliou, Amalia; Pleros, Nikos
2014-03-01
Towards achieving a functional RAM organization that reaps the advantages offered by optical technology, a complete set of optical peripheral modules, namely the Row (RD) and Column Decoder (CD) units, is required. In this perspective, we demonstrate an all-passive 2×4 optical RAM RD with row access operation and subsequent all-passive column decoding to control the access of WDM-formatted words in optical RAM rows. The 2×4 RD exploits a WDM-formatted 2-bit-long memory WordLine address along with its complementary value, all of them encoded on four different wavelengths and broadcasted to all RAM rows. The RD relies on an all-passive wavelength-selective filtering matrix (λ-matrix) that ensures a logical `0' output only at the selected RAM row. Subsequently, the RD output of each row drives the respective SOA-MZI-based Row Access Gate (AG) to grant/block the entry of the incoming data words to the whole memory row. In case of a selected row, the data word exits the row AG and enters the respective CD that relies on an allpassive wavelength-selective Arrayed Waveguide Grating (AWG) for decoding the word bits into their individual columns. Both RD and CD procedures are carried out without requiring any active devices, assuming that the memory address and data word bits as well as their inverted values will be available in their optical form by the CPU interface. Proof-of-concept experimental verification exploiting cascaded pairs of AWGs as the λ-matrix is demonstrated at 10Gb/s, providing error-free operation with a peak power penalty lower than 0.2dB for all optical word channels.
A One-Pass Real-Time Decoder Using Memory-Efficient State Network
Shao, Jian; Li, Ta; Zhang, Qingqing; Zhao, Qingwei; Yan, Yonghong
This paper presents our developed decoder which adopts the idea of statically optimizing part of the knowledge sources while handling the others dynamically. The lexicon, phonetic contexts and acoustic model are statically integrated to form a memory-efficient state network, while the language model (LM) is dynamically incorporated on the fly by means of extended tokens. The novelties of our approach for constructing the state network are (1) introducing two layers of dummy nodes to cluster the cross-word (CW) context dependent fan-in and fan-out triphones, (2) introducing a so-called “WI layer” to store the word identities and putting the nodes of this layer in the non-shared mid-part of the network, (3) optimizing the network at state level by a sufficient forward and backward node-merge process. The state network is organized as a multi-layer structure for distinct token propagation at each layer. By exploiting the characteristics of the state network, several techniques including LM look-ahead, LM cache and beam pruning are specially designed for search efficiency. Especially in beam pruning, a layer-dependent pruning method is proposed to further reduce the search space. The layer-dependent pruning takes account of the neck-like characteristics of WI layer and the reduced variety of word endings, which enables tighter beam without introducing much search errors. In addition, other techniques including LM compression, lattice-based bookkeeping and lattice garbage collection are also employed to reduce the memory requirements. Experiments are carried out on a Mandarin spontaneous speech recognition task where the decoder involves a trigram LM and CW triphone models. A comparison with HDecode of HTK toolkits shows that, within 1% performance deviation, our decoder can run 5 times faster with half of the memory footprint.
Energy Technology Data Exchange (ETDEWEB)
Vinyard, Natalia Sergeevna [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Perry, Theodore Sonne [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Usov, Igor Olegovich [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2017-10-04
We calculate opacity from k (hn)=-ln[T(hv)]/pL, where T(hv) is the transmission for photon energy hv, p is sample density, and L is path length through the sample. The density and path length are measured together by Rutherford backscatter. Δk = $\\partial k$\\ $\\partial T$ ΔT + $\\partial k$\\ $\\partial (pL)$. We can re-write this in terms of fractional error as Δk/k = Δ1n(T)/T + Δ(pL)/(pL). Transmission itself is calculated from T=(U-E)/(V-E)=B/B0, where B is transmitted backlighter (BL) signal and B_{0} is unattenuated backlighter signal. Then ΔT/T=Δln(T)=ΔB/B+ΔB_{0}/B_{0}, and consequently Δk/k = 1/T (ΔB/B + ΔB$_0$/B$_0$ + Δ(pL)/(pL). Transmission is measured in the range of 0.2
Decoding reality the universe as quantum information
Vedral, Vlatko
2010-01-01
In Decoding Reality, Vlatko Vedral offers a mind-stretching look at the deepest questions about the universe--where everything comes from, why things are as they are, what everything is. The most fundamental definition of reality is not matter or energy, he writes, but information--and it is the processing of information that lies at the root of all physical, biological, economic, and social phenomena. This view allows Vedral to address a host of seemingly unrelated questions: Why does DNA bind like it does? What is the ideal diet for longevity? How do you make your first million dollars? We can unify all through the understanding that everything consists of bits of information, he writes, though that raises the question of where these bits come from. To find the answer, he takes us on a guided tour through the bizarre realm of quantum physics. At this sub-sub-subatomic level, we find such things as the interaction of separated quantum particles--what Einstein called "spooky action at a distance." In fact, V...
Statistical coding and decoding of heartbeat intervals.
Lucena, Fausto; Barros, Allan Kardec; Príncipe, José C; Ohnishi, Noboru
2011-01-01
The heart integrates neuroregulatory messages into specific bands of frequency, such that the overall amplitude spectrum of the cardiac output reflects the variations of the autonomic nervous system. This modulatory mechanism seems to be well adjusted to the unpredictability of the cardiac demand, maintaining a proper cardiac regulation. A longstanding theory holds that biological organisms facing an ever-changing environment are likely to evolve adaptive mechanisms to extract essential features in order to adjust their behavior. The key question, however, has been to understand how the neural circuitry self-organizes these feature detectors to select behaviorally relevant information. Previous studies in computational perception suggest that a neural population enhances information that is important for survival by minimizing the statistical redundancy of the stimuli. Herein we investigate whether the cardiac system makes use of a redundancy reduction strategy to regulate the cardiac rhythm. Based on a network of neural filters optimized to code heartbeat intervals, we learn a population code that maximizes the information across the neural ensemble. The emerging population code displays filter tuning proprieties whose characteristics explain diverse aspects of the autonomic cardiac regulation, such as the compromise between fast and slow cardiac responses. We show that the filters yield responses that are quantitatively similar to observed heart rate responses during direct sympathetic or parasympathetic nerve stimulation. Our findings suggest that the heart decodes autonomic stimuli according to information theory principles analogous to how perceptual cues are encoded by sensory systems.
Rate Aware Instantly Decodable Network Codes
Douik, Ahmed
2016-02-26
This paper addresses the problem of reducing the delivery time of data messages to cellular users using instantly decodable network coding (IDNC) with physical-layer rate awareness. While most of the existing literature on IDNC does not consider any physical layer complications, this paper proposes a cross-layer scheme that incorporates the different channel rates of the various users in the decision process of both the transmitted message combinations and the rates with which they are transmitted. The completion time minimization problem in such scenario is first shown to be intractable. The problem is, thus, approximated by reducing, at each transmission, the increase of an anticipated version of the completion time. The paper solves the problem by formulating it as a maximum weight clique problem over a newly designed rate aware IDNC (RA-IDNC) graph. Further, the paper provides a multi-layer solution to improve the completion time approximation. Simulation results suggest that the cross-layer design largely outperforms the uncoded transmissions strategies and the classical IDNC scheme. © 2015 IEEE.
Encoding and decoding messages with chaotic lasers
International Nuclear Information System (INIS)
Alsing, P.M.; Gavrielides, A.; Kovanis, V.; Roy, R.; Thornburg, K.S. Jr.
1997-01-01
We investigate the structure of the strange attractor of a chaotic loss-modulated solid-state laser utilizing return maps based on a combination of intensity maxima and interspike intervals, as opposed to those utilizing Poincare sections defined by the intensity maxima of the laser (I=0,Ie<0) alone. We find both experimentally and numerically that a simple, intrinsic relationship exists between an intensity maximum and the pair of preceding and succeeding interspike intervals. In addition, we numerically investigate encoding messages on the output of a chaotic transmitter laser and its subsequent decoding by a similar receiver laser. By exploiting the relationship between the intensity maxima and the interspike intervals, we demonstrate that the method utilized to encode the message is vital to the system close-quote s ability to hide the signal from unwanted deciphering. In this work alternative methods are studied in order to encode messages by modulating the magnitude of pumping of the transmitter laser and also by driving its loss modulation with more than one frequency. copyright 1997 The American Physical Society
Fast mental states decoding in mixed reality.
Directory of Open Access Journals (Sweden)
Daniele eDe Massari
2014-11-01
Full Text Available The combination of Brain-Computer Interface technology, allowing online monitoring and decoding of brain activity, with virtual and mixed reality systems may help to shape and guide implicit and explicit learning using ecological scenarios. Real-time information of ongoing brain states acquired through BCI might be exploited for controlling data presentation in virtual environments. In this context, assessing to what extent brain states can be discriminated during mixed reality experience is critical for adapting specific data features to contingent brain activity. In this study we recorded EEG data while participants experienced a mixed reality scenario implemented through the eXperience Induction Machine (XIM. The XIM is a novel framework modeling the integration of a sensing system that evaluates and measures physiological and psychological states with a number of actuators and effectors that coherently reacts to the user's actions. We then assessed continuous EEG-based discrimination of spatial navigation, reading and calculation performed in mixed reality, using LDA and SVM classifiers. Dynamic single trial classification showed high accuracy of LDA and SVM classifiers in detecting multiple brain states as well as in differentiating between high and low mental workload, using a 5 s time-window shifting every 200 ms. Our results indicate overall better performance of LDA with respect to SVM and suggest applicability of our approach in a BCI-controlled mixed reality scenario. Ultimately, successful prediction of brain states might be used to drive adaptation of data representation in order to boost information processing in mixed reality.
Decoding P4-ATPase substrate interactions.
Roland, Bartholomew P; Graham, Todd R
Cellular membranes display a diversity of functions that are conferred by the unique composition and organization of their proteins and lipids. One important aspect of lipid organization is the asymmetric distribution of phospholipids (PLs) across the plasma membrane. The unequal distribution of key PLs between the cytofacial and exofacial leaflets of the bilayer creates physical surface tension that can be used to bend the membrane; and like Ca 2+ , a chemical gradient that can be used to transduce biochemical signals. PL flippases in the type IV P-type ATPase (P4-ATPase) family are the principle transporters used to set and repair this PL gradient and the asymmetric organization of these membranes are encoded by the substrate specificity of these enzymes. Thus, understanding the mechanisms of P4-ATPase substrate specificity will help reveal their role in membrane organization and cell biology. Further, decoding the structural determinants of substrate specificity provides investigators the opportunity to mutationally tune this specificity to explore the role of particular PL substrates in P4-ATPase cellular functions. This work reviews the role of P4-ATPases in membrane biology, presents our current understanding of P4-ATPase substrate specificity, and discusses how these fundamental aspects of P4-ATPase enzymology may be used to enhance our knowledge of cellular membrane biology.
Fast mental states decoding in mixed reality.
De Massari, Daniele; Pacheco, Daniel; Malekshahi, Rahim; Betella, Alberto; Verschure, Paul F M J; Birbaumer, Niels; Caria, Andrea
2014-01-01
The combination of Brain-Computer Interface (BCI) technology, allowing online monitoring and decoding of brain activity, with virtual and mixed reality (MR) systems may help to shape and guide implicit and explicit learning using ecological scenarios. Real-time information of ongoing brain states acquired through BCI might be exploited for controlling data presentation in virtual environments. Brain states discrimination during mixed reality experience is thus critical for adapting specific data features to contingent brain activity. In this study we recorded electroencephalographic (EEG) data while participants experienced MR scenarios implemented through the eXperience Induction Machine (XIM). The XIM is a novel framework modeling the integration of a sensing system that evaluates and measures physiological and psychological states with a number of actuators and effectors that coherently reacts to the user's actions. We then assessed continuous EEG-based discrimination of spatial navigation, reading and calculation performed in MR, using linear discriminant analysis (LDA) and support vector machine (SVM) classifiers. Dynamic single trial classification showed high accuracy of LDA and SVM classifiers in detecting multiple brain states as well as in differentiating between high and low mental workload, using a 5 s time-window shifting every 200 ms. Our results indicate overall better performance of LDA with respect to SVM and suggest applicability of our approach in a BCI-controlled MR scenario. Ultimately, successful prediction of brain states might be used to drive adaptation of data representation in order to boost information processing in MR.
Rate Aware Instantly Decodable Network Codes
Douik, Ahmed; Sorour, Sameh; Al-Naffouri, Tareq Y.; Alouini, Mohamed-Slim
2016-01-01
This paper addresses the problem of reducing the delivery time of data messages to cellular users using instantly decodable network coding (IDNC) with physical-layer rate awareness. While most of the existing literature on IDNC does not consider any physical layer complications, this paper proposes a cross-layer scheme that incorporates the different channel rates of the various users in the decision process of both the transmitted message combinations and the rates with which they are transmitted. The completion time minimization problem in such scenario is first shown to be intractable. The problem is, thus, approximated by reducing, at each transmission, the increase of an anticipated version of the completion time. The paper solves the problem by formulating it as a maximum weight clique problem over a newly designed rate aware IDNC (RA-IDNC) graph. Further, the paper provides a multi-layer solution to improve the completion time approximation. Simulation results suggest that the cross-layer design largely outperforms the uncoded transmissions strategies and the classical IDNC scheme. © 2015 IEEE.
Statistical coding and decoding of heartbeat intervals.
Directory of Open Access Journals (Sweden)
Fausto Lucena
Full Text Available The heart integrates neuroregulatory messages into specific bands of frequency, such that the overall amplitude spectrum of the cardiac output reflects the variations of the autonomic nervous system. This modulatory mechanism seems to be well adjusted to the unpredictability of the cardiac demand, maintaining a proper cardiac regulation. A longstanding theory holds that biological organisms facing an ever-changing environment are likely to evolve adaptive mechanisms to extract essential features in order to adjust their behavior. The key question, however, has been to understand how the neural circuitry self-organizes these feature detectors to select behaviorally relevant information. Previous studies in computational perception suggest that a neural population enhances information that is important for survival by minimizing the statistical redundancy of the stimuli. Herein we investigate whether the cardiac system makes use of a redundancy reduction strategy to regulate the cardiac rhythm. Based on a network of neural filters optimized to code heartbeat intervals, we learn a population code that maximizes the information across the neural ensemble. The emerging population code displays filter tuning proprieties whose characteristics explain diverse aspects of the autonomic cardiac regulation, such as the compromise between fast and slow cardiac responses. We show that the filters yield responses that are quantitatively similar to observed heart rate responses during direct sympathetic or parasympathetic nerve stimulation. Our findings suggest that the heart decodes autonomic stimuli according to information theory principles analogous to how perceptual cues are encoded by sensory systems.
Mechanism of recycling of post-termination ribosomal complexes in ...
Indian Academy of Sciences (India)
Madhu
all pathway of ribosome recycling in eubacteria with especial reference to the important role of the initiation factor ... [Seshadri A and Varshney U 2006 Mechanism of recycling of post-termination ribosomal complexes in eubacteria: a new role of initiation factor 3 .... RRF binding results in a remarkable conformational change.
Expression of protein-coding genes embedded in ribosomal DNA
DEFF Research Database (Denmark)
Johansen, Steinar D; Haugen, Peik; Nielsen, Henrik
2007-01-01
Ribosomal DNA (rDNA) is a specialised chromosomal location that is dedicated to high-level transcription of ribosomal RNA genes. Interestingly, rDNAs are frequently interrupted by parasitic elements, some of which carry protein genes. These are non-LTR retrotransposons and group II introns that e...... in the nucleolus....
Proto-ribosome: a theoretical approach based on RNA relics
Demongeot, Jacques
2017-01-01
We describe in this paper, based on already published articles, a contribution to the theory postulating the existence of a proto-ribosome, which could have appeared early at the origin of life and we discuss the interest of this notion in an evolutionary perspective, taking into account the existence of possible RNA relics of this proto-ribosome.
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
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.
Macrolide antibiotic interaction and resistance on the bacterial ribosome.
Poehlsgaard, Jacob; Douthwaite, Stephen
2003-02-01
Our understanding of the fine structure of many antibiotic target sites has reached a new level of enlightenment in the last couple of years due to the advent, by X-ray crystallography, of high-resolution structures of the bacterial ribosome. Many classes of clinically useful antibiotics bind to the ribosome to inhibit bacterial protein synthesis. Macrolide, lincosamide and streptogramin B (MLSB) antibiotics form one of the largest groups, and bind to the same site on the 50S ribosomal subunit. Here, we review the molecular details of the ribosomal MLSB site to put into perspective the main points from a wealth of biochemical and genetic data that have been collected over several decades. The information is now available to understand, at atomic resolution, how macrolide antibiotics interact with their ribosomal target, how the target is altered to confer resistance, and in which directions we need to look if we are to rationally design better drugs to overcome the extant resistance mechanisms.
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.
An investigation of error correcting techniques for OMV and AXAF
Ingels, Frank; Fryer, John
1991-01-01
The original objectives of this project were to build a test system for the NASA 255/223 Reed/Solomon encoding/decoding chip set and circuit board. This test system was then to be interfaced with a convolutional system at MSFC to examine the performance of the concantinated codes. After considerable work, it was discovered that the convolutional system could not function as needed. This report documents the design, construction, and testing of the test apparatus for the R/S chip set. The approach taken was to verify the error correcting behavior of the chip set by injecting known error patterns onto data and observing the results. Error sequences were generated using pseudo-random number generator programs, with Poisson time distribution between errors and Gaussian burst lengths. Sample means, variances, and number of un-correctable errors were calculated for each data set before testing.
Control of Ribosome Synthesis in Escherichia coli
DEFF Research Database (Denmark)
Molin, Søren; Meyenburg, K. von; Måløe, O.
1977-01-01
The rate of ribosome synthesis and accumulation in Escherichia coli during the transition after an energy source shift-down was analyzed. The shift was imposed on cultures of stringent and relaxed strains growing in glucose minimal medium by the addition of the glucose analogue {alpha...... and to estimate the transcription time for the rRNA operon under different conditions. In steady states of growth with growth rates ranging from 0.75 to 2.3 doublings/h, as well as during the transition after a shift-down, the transcription time of the rRNA operon was constant. The rate of synthesis of r......RNA correlated during this transition – in contrast to the rate of accumulation (M. T. Hansen et al., J. Bacteriol. 122: 585-591, 1975) – with the ppGpp pool in the same way as has been observed during partial amino acid starvation....
Progressive and Error-Resilient Transmission Strategies for VLC Encoded Signals over Noisy Channels
Directory of Open Access Journals (Sweden)
Guillemot Christine
2006-01-01
Full Text Available This paper addresses the issue of robust and progressive transmission of signals (e.g., images, video encoded with variable length codes (VLCs over error-prone channels. This paper first describes bitstream construction methods offering good properties in terms of error resilience and progressivity. In contrast with related algorithms described in the literature, all proposed methods have a linear complexity as the sequence length increases. The applicability of soft-input soft-output (SISO and turbo decoding principles to resulting bitstream structures is investigated. In addition to error resilience, the amenability of the bitstream construction methods to progressive decoding is considered. The problem of code design for achieving good performance in terms of error resilience and progressive decoding with these transmission strategies is then addressed. The VLC code has to be such that the symbol energy is mainly concentrated on the first bits of the symbol representation (i.e., on the first transitions of the corresponding codetree. Simulation results reveal high performance in terms of symbol error rate (SER and mean-square reconstruction error (MSE. These error-resilience and progressivity properties are obtained without any penalty in compression efficiency. Codes with such properties are of strong interest for the binarization of -ary sources in state-of-the-art image, and video coding systems making use of, for example, the EBCOT or CABAC algorithms. A prior statistical analysis of the signal allows the construction of the appropriate binarization code.
Iterative Sparse Channel Estimation and Decoding for Underwater MIMO-OFDM
Directory of Open Access Journals (Sweden)
Berger ChristianR
2010-01-01
Full Text Available We propose a block-by-block iterative receiver for underwater MIMO-OFDM that couples channel estimation with multiple-input multiple-output (MIMO detection and low-density parity-check (LDPC channel decoding. In particular, the channel estimator is based on a compressive sensing technique to exploit the channel sparsity, the MIMO detector consists of a hybrid use of successive interference cancellation and soft minimum mean-square error (MMSE equalization, and channel coding uses nonbinary LDPC codes. Various feedback strategies from the channel decoder to the channel estimator are studied, including full feedback of hard or soft symbol decisions, as well as their threshold-controlled versions. We study the receiver performance using numerical simulation and experimental data collected from the RACE08 and SPACE08 experiments. We find that iterative receiver processing including sparse channel estimation leads to impressive performance gains. These gains are more pronounced when the number of available pilots to estimate the channel is decreased, for example, when a fixed number of pilots is split between an increasing number of parallel data streams in MIMO transmission. For the various feedback strategies for iterative channel estimation, we observe that soft decision feedback slightly outperforms hard decision feedback.
Directory of Open Access Journals (Sweden)
Savitha H. M.
2010-09-01
Full Text Available A comparison of the performance of hard and soft-decision turbo coded Orthogonal Frequency Division Multiplexing systems with Quadrature Phase Shift Keying (QPSK and 16-Quadrature Amplitude Modulation (16-QAM is considered in the first section of this paper. The results show that the soft-decision method greatly outperforms the hard-decision method. The complexity of the demapper is reduced with the use of simplified algorithm for 16-QAM demapping. In the later part of the paper, we consider the transmission of data over additive white class A noise (AWAN channel, using turbo coded QPSK and 16-QAM systems. We propose a novel turbo decoding scheme for AWAN channel. Also we compare the performance of turbo coded systems with QPSK and 16-QAM on AWAN channel with two different channel values- one computed as per additive white Gaussian noise (AWGN channel conditions and the other as per AWAN channel conditions. The results show that the use of appropriate channel value in turbo decoding helps to combat the impulsive noise more effectively. The proposed model for AWAN channel exhibits comparable Bit error rate (BER performance as compared to AWGN channel.
Biedka, Stephanie; Micic, Jelena; Wilson, Daniel; Brown, Hailey; Diorio-Toth, Luke; Woolford, John L
2018-04-24
Ribosome biogenesis involves numerous preribosomal RNA (pre-rRNA) processing events to remove internal and external transcribed spacer sequences, ultimately yielding three mature rRNAs. Removal of the internal transcribed spacer 2 spacer RNA is the final step in large subunit pre-rRNA processing and begins with endonucleolytic cleavage at the C 2 site of 27SB pre-rRNA. C 2 cleavage requires the hierarchical recruitment of 11 ribosomal proteins and 14 ribosome assembly factors. However, the function of these proteins in C 2 cleavage remained unclear. In this study, we have performed a detailed analysis of the effects of depleting proteins required for C 2 cleavage and interpreted these results using cryo-electron microscopy structures of assembling 60S subunits. This work revealed that these proteins are required for remodeling of several neighborhoods, including two major functional centers of the 60S subunit, suggesting that these remodeling events form a checkpoint leading to C 2 cleavage. Interestingly, when C 2 cleavage is directly blocked by depleting or inactivating the C 2 endonuclease, assembly progresses through all other subsequent steps. © 2018 Biedka et al.
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.
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.
An evaluation of the effect of JPEG, JPEG2000, and H.264/AVC on CQR codes decoding process
Vizcarra Melgar, Max E.; Farias, Mylène C. Q.; Zaghetto, Alexandre
2015-02-01
This paper presents a binarymatrix code based on QR Code (Quick Response Code), denoted as CQR Code (Colored Quick Response Code), and evaluates the effect of JPEG, JPEG2000 and H.264/AVC compression on the decoding process. The proposed CQR Code has three additional colors (red, green and blue), what enables twice as much storage capacity when compared to the traditional black and white QR Code. Using the Reed-Solomon error-correcting code, the CQR Code model has a theoretical correction capability of 38.41%. The goal of this paper is to evaluate the effect that degradations inserted by common image compression algorithms have on the decoding process. Results show that a successful decoding process can be achieved for compression rates up to 0.3877 bits/pixel, 0.1093 bits/pixel and 0.3808 bits/pixel for JPEG, JPEG2000 and H.264/AVC formats, respectively. The algorithm that presents the best performance is the H.264/AVC, followed by the JPEG2000, and JPEG.
International Nuclear Information System (INIS)
Lott, Brittany Burton; Wang, Yongmei; Nakazato, Takuya
2013-01-01
Assembly of the ribosome from its protein and RNA constituents must occur quickly and efficiently in order to synthesize the proteins necessary for all cellular activity. Since the early 1960’s, certain characteristics of possible assembly pathways have been elucidated, yet the mechanisms that govern the precise recognition events remain unclear. We utilize a comparative analysis to investigate the amino acid composition of ribosomal proteins (r-proteins) with respect to their role in the assembly process. We compared small subunit (30S) r-protein sequences to those of other housekeeping proteins from 560 bacterial species and searched for correlations between r-protein amino acid content and factors such as assembly binding order, environmental growth temperature, protein size, and contact with ribosomal RNA (rRNA) in the 30S complex. We find r-proteins have a significantly high percent of positive residues, which are highly represented at rRNA contact sites. An inverse correlation between the percent of positive residues and r-protein size was identified and is mainly due to the content of Lysine residues, rather than Arginine. Nearly all r-proteins carry a net positive charge, but no statistical correlation between the net charge and the binding order was detected. Thermophilic (high-temperature) r-proteins contain increased Arginine, Isoleucine, and Tyrosine, and decreased Serine and Threonine compared to mesophilic (lower-temperature), reflecting a known distinction between thermophiles and mesophiles, possibly to account for protein thermostability. However, this difference in amino acid content does not extend to rRNA contact sites, as the proportions of thermophilic and mesophilic contact residues are not significantly different. Given the significantly higher level of positively charged residues in r-proteins and at contact sites, we conclude that ribosome assembly relies heavily on an electrostatic component of interaction. However, the binding order of
On the control of ribosomal protein biosynthesis in Escherichia coli
International Nuclear Information System (INIS)
Pichon, J.; Marvaldi, J.; Coeroli, C.; Cozzone, A.; Marchis-Mouren, G.
1977-01-01
The rate of individual ribosomal protein synthesis relative to total protein synthesis has been determined in Escherichia coli rel + and rel - cells, under valyl-tRNA deprivation. These strains have a temperature-sensitive valyl-tRNA synthetase. Starvation was obtained following transfer of the cells to non-permissive temperature. Ribosomal proteins were obtained by treatment of either total lysates of freeze-thawed lysozyme spheroplasts or ammonium sulphate precipitate of ribosomes, with acetic acid. Differential labelling of the ribosomal proteins was observed in both strains: proteins from the rel + strain appear more labelled than those from the rel - strain, the rate of labelling of individual proteins being about the same in both strains. Moreover ribosomal proteins were found as stable during starvation as total protein. It is thus concluded that in starving cells individual ribosomal proteins are not synthesized at equal rates. This indicates that the synthesis of ribosomal proteins is not only under the control of the rel gene
Post-transcriptional regulation of ribosome biogenesis in yeast
Directory of Open Access Journals (Sweden)
Isabelle C. Kos-Braun
2017-05-01
Full Text Available Most microorganisms are exposed to the constantly and often rapidly changing environment. As such they evolved mechanisms to balance their metabolism and energy expenditure with the resources available to them. When resources become scarce or conditions turn out to be unfavourable for growth, cells reduce their metabolism and energy usage to survive. One of the major energy consuming processes in the cell is ribosome biogenesis. Unsurprisingly, cells encountering adverse conditions immediately shut down production of new ribosomes. It is well established that nutrient depletion leads to a rapid repression of transcription of the genes encoding ribosomal proteins, ribosome biogenesis factors as well as ribosomal RNA (rRNA. However, if pre-rRNA processing and ribosome assembly are regulated post-transcriptionally remains largely unclear. We have recently uncovered that the yeast Saccharomyces cerevisiae rapidly switches between two alternative pre-rRNA processing pathways depending on the environmental conditions. Our findings reveal a new level of complexity in the regulation of ribosome biogenesis.
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
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.
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.
No-reference analysis of decoded MPEG images for PSNR estimation and post-processing
DEFF Research Database (Denmark)
Forchhammer, Søren; Li, Huiying; Andersen, Jakob Dahl
2011-01-01
We propose no-reference analysis and processing of DCT (Discrete Cosine Transform) coded images based on estimation of selected MPEG parameters from the decoded video. The goal is to assess MPEG video quality and perform post-processing without access to neither the original stream nor the code...... stream. Solutions are presented for MPEG-2 video. A method to estimate the quantization parameters of DCT coded images and MPEG I-frames at the macro-block level is presented. The results of this analysis is used for deblocking and deringing artifact reduction and no-reference PSNR estimation without...... code stream access. An adaptive deringing method using texture classification is presented. On the test set, the quantization parameters in MPEG-2 I-frames are estimated with an overall accuracy of 99.9% and the PSNR is estimated with an overall average error of 0.3dB. The deringing and deblocking...
Improved Iterative Decoding of Network-Channel Codes for Multiple-Access Relay Channel.
Majumder, Saikat; Verma, Shrish
2015-01-01
Cooperative communication using relay nodes is one of the most effective means of exploiting space diversity for low cost nodes in wireless network. In cooperative communication, users, besides communicating their own information, also relay the information of other users. In this paper we investigate a scheme where cooperation is achieved using a common relay node which performs network coding to provide space diversity for two information nodes transmitting to a base station. We propose a scheme which uses Reed-Solomon error correcting code for encoding the information bit at the user nodes and convolutional code as network code, instead of XOR based network coding. Based on this encoder, we propose iterative soft decoding of joint network-channel code by treating it as a concatenated Reed-Solomon convolutional code. Simulation results show significant improvement in performance compared to existing scheme based on compound codes.
Optical LDPC decoders for beyond 100 Gbits/s optical transmission.
Djordjevic, Ivan B; Xu, Lei; Wang, Ting
2009-05-01
We present an optical low-density parity-check (LDPC) decoder suitable for implementation above 100 Gbits/s, which provides large coding gains when based on large-girth LDPC codes. We show that a basic building block, the probabilities multiplier circuit, can be implemented using a Mach-Zehnder interferometer, and we propose corresponding probabilistic-domain sum-product algorithm (SPA). We perform simulations of a fully parallel implementation employing girth-10 LDPC codes and proposed SPA. The girth-10 LDPC(24015,19212) code of the rate of 0.8 outperforms the BCH(128,113)xBCH(256,239) turbo-product code of the rate of 0.82 by 0.91 dB (for binary phase-shift keying at 100 Gbits/s and a bit error rate of 10(-9)), and provides a net effective coding gain of 10.09 dB.
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.
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...
Decoding ensemble activity from neurophysiological recordings in the temporal cortex.
Kreiman, Gabriel
2011-01-01
We study subjects with pharmacologically intractable epilepsy who undergo semi-chronic implantation of electrodes for clinical purposes. We record physiological activity from tens to more than one hundred electrodes implanted in different parts of neocortex. These recordings provide higher spatial and temporal resolution than non-invasive measures of human brain activity. Here we discuss our efforts to develop hardware and algorithms to interact with the human brain by decoding ensemble activity in single trials. We focus our discussion on decoding visual information during a variety of visual object recognition tasks but the same technologies and algorithms can also be directly applied to other cognitive phenomena.
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
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....
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
Cisplatin Targeting of Bacterial Ribosomal RNA Hairpins
Directory of Open Access Journals (Sweden)
Gayani N. P. Dedduwa-Mudalige
2015-09-01
Full Text Available Cisplatin is a clinically important chemotherapeutic agent known to target purine bases in nucleic acids. In addition to major deoxyribonucleic acid (DNA intrastrand cross-links, cisplatin also forms stable adducts with many types of ribonucleic acid (RNA including siRNA, spliceosomal RNAs, tRNA, and rRNA. All of these RNAs play vital roles in the cell, such as catalysis of protein synthesis by rRNA, and therefore serve as potential drug targets. This work focused on platination of two highly conserved RNA hairpins from E. coli ribosomes, namely pseudouridine-modified helix 69 from 23S rRNA and the 790 loop of helix 24 from 16S rRNA. RNase T1 probing, MALDI mass spectrometry, and dimethyl sulfate mapping revealed platination at GpG sites. Chemical probing results also showed platination-induced RNA structural changes. These findings reveal solvent and structural accessibility of sites within bacterial RNA secondary structures that are functionally significant and therefore viable targets for cisplatin as well as other classes of small molecules. Identifying target preferences at the nucleotide level, as well as determining cisplatin-induced RNA conformational changes, is important for the design of more potent drug molecules. Furthermore, the knowledge gained through studies of RNA-targeting by cisplatin is applicable to a broad range of organisms from bacteria to human.
Organization of Replication of Ribosomal DNA in Saccharomyces cerevisiae
Linskens, Maarten H.K.; Huberman, Joel A.
1988-01-01
Using recently developed replicon mapping techniques, we have analyzed the replication of the ribosomal DNA in Saccharomyces cerevisiae. The results show that (i) the functional origin of replication colocalizes with an autonomously replicating sequence element previously mapped to the
Ribosome slowed by mutation to streptomycin resistance. [Escherichia coli
Energy Technology Data Exchange (ETDEWEB)
Galas, D J; Branscomb, E W
1976-08-12
The effect of mutation to streptomycin resistance on the speed of polypeptide elongation in Escherichia coli was investigated. Translation speed was determined by measuring the time required for the first newly synthesized ..beta..-galactosidase molecules to appear after induction of the lactose operon. The results showed that ribosome speed is not a fixed parameter inherent to the protein synthetic apparatus, but a variable determined by the kinetics of translation and ultimately by the structure of the ribosome. (HLW)
Defective ribosome assembly in Shwachman-Diamond syndrome.
Wong, Chi C; Traynor, David; Basse, Nicolas; Kay, Robert R; Warren, Alan J
2011-10-20
Shwachman-Diamond syndrome (SDS), a recessive leukemia predisposition disorder characterized by bone marrow failure, exocrine pancreatic insufficiency, skeletal abnormalities and poor growth, is caused by mutations in the highly conserved SBDS gene. Here, we test the hypothesis that defective ribosome biogenesis underlies the pathogenesis of SDS. We create conditional mutants in the essential SBDS ortholog of the ancient eukaryote Dictyostelium discoideum using temperature-sensitive, self-splicing inteins, showing that mutant cells fail to grow at the restrictive temperature because ribosomal subunit joining is markedly impaired. Remarkably, wild type human SBDS complements the growth and ribosome assembly defects in mutant Dictyostelium cells, but disease-associated human SBDS variants are defective. SBDS directly interacts with the GTPase elongation factor-like 1 (EFL1) on nascent 60S subunits in vivo and together they catalyze eviction of the ribosome antiassociation factor eukaryotic initiation factor 6 (eIF6), a prerequisite for the translational activation of ribosomes. Importantly, lymphoblasts from SDS patients harbor a striking defect in ribosomal subunit joining whose magnitude is inversely proportional to the level of SBDS protein. These findings in Dictyostelium and SDS patient cells provide compelling support for the hypothesis that SDS is a ribosomopathy caused by corruption of an essential cytoplasmic step in 60S subunit maturation.
Emerging functions of ribosomal proteins in gene-specific transcription and translation
International Nuclear Information System (INIS)
Lindstroem, Mikael S.
2009-01-01
Ribosomal proteins have remained highly conserved during evolution presumably reflecting often critical functions in ribosome biogenesis or mature ribosome function. In addition, several ribosomal proteins possess distinct extra-ribosomal functions in apoptosis, DNA repair and transcription. An increasing number of ribosomal proteins have been shown to modulate the trans-activation function of important regulatory proteins such as NF-κB, p53, c-Myc and nuclear receptors. Furthermore, a subset of ribosomal proteins can bind directly to untranslated regions of mRNA resulting in transcript-specific translational control outside of the ribosome itself. Collectively, these findings suggest that ribosomal proteins may have a wider functional repertoire within the cell than previously thought. The future challenge is to identify and validate these novel functions in the background of an often essential primary function in ribosome biogenesis and cell growth.
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.
Decoding Representations: How Children with Autism Understand Drawings
Allen, Melissa L.
2009-01-01
Young typically developing children can reason about abstract depictions if they know the intention of the artist. Children with autism spectrum disorder (ASD), who are notably impaired in social, "intention monitoring" domains, may have great difficulty in decoding vague representations. In Experiment 1, children with ASD are unable to use…
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.
The Fluid Reading Primer: Animated Decoding Support for Emergent Readers.
Zellweger, Polle T.; Mackinlay, Jock D.
A prototype application called the Fluid Reading Primer was developed to help emergent readers with the process of decoding written words into their spoken forms. The Fluid Reading Primer is part of a larger research project called Fluid Documents, which is exploring the use of interactive animation of typography to show additional information in…
Tracking Perceptual and Memory Decisions by Decoding Brain Activity
van Vugt, Marieke; Brandt, Armin; Schulze-Bonhage, Andreas
2017-01-01
Decision making is thought to involve a process of evidence accumulation, modelled as a drifting diffusion process. This modeling framework suggests that all single-stage decisions involve a similar evidence accumulation process. In this paper we use decoding by machine learning classifiers on
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.
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.
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.
Name that tune: decoding music from the listening brain.
Schaefer, R.S.; Farquhar, J.D.R.; Blokland, Y.M.; Sadakata, M.; Desain, P.W.M.
2011-01-01
In the current study we use electroencephalography (EEG) to detect heard music from the brain signal, hypothesizing that the time structure in music makes it especially suitable for decoding perception from EEG signals. While excluding music with vocals, we classified the perception of seven
Name that tune: Decoding music from the listening brain
Schaefer, R.S.; Farquhar, J.D.R.; Blokland, Y.M.; Sadakata, M.; Desain, P.W.M.
2011-01-01
In the current study we use electroencephalography (EEG) to detect heard music from the brain signal, hypothesizing that the time structure in music makes it especially suitable for decoding perception from EEG signals. While excluding music with vocals, we classified the perception of seven
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.
O2-GIDNC: Beyond instantly decodable network coding
Aboutorab, Neda; Sorour, Sameh; Sadeghi, Parastoo
2013-01-01
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
EEG source imaging assists decoding in a face recognition task
DEFF Research Database (Denmark)
Andersen, Rasmus S.; Eliasen, Anders U.; Pedersen, Nicolai
2017-01-01
of face recognition. This task concerns the differentiation of brain responses to images of faces and scrambled faces and poses a rather difficult decoding problem at the single trial level. We implement the pipeline using spatially focused features and show that this approach is challenged and source...
Ultrahigh Error Threshold for Surface Codes with Biased Noise
Tuckett, David K.; Bartlett, Stephen D.; Flammia, Steven T.
2018-02-01
We show that a simple modification of the surface code can exhibit an enormous gain in the error correction threshold for a noise model in which Pauli Z errors occur more frequently than X or Y errors. Such biased noise, where dephasing dominates, is ubiquitous in many quantum architectures. In the limit of pure dephasing noise we find a threshold of 43.7(1)% using a tensor network decoder proposed by Bravyi, Suchara, and Vargo. The threshold remains surprisingly large in the regime of realistic noise bias ratios, for example 28.2(2)% at a bias of 10. The performance is, in fact, at or near the hashing bound for all values of the bias. The modified surface code still uses only weight-4 stabilizers on a square lattice, but merely requires measuring products of Y instead of Z around the faces, as this doubles the number of useful syndrome bits associated with the dominant Z errors. Our results demonstrate that large efficiency gains can be found by appropriately tailoring codes and decoders to realistic noise models, even under the locality constraints of topological codes.
Error Correction for Non-Abelian Topological Quantum Computation
Directory of Open Access Journals (Sweden)
James R. Wootton
2014-03-01
Full Text Available The possibility of quantum computation using non-Abelian anyons has been considered for over a decade. However, the question of how to obtain and process information about what errors have occurred in order to negate their effects has not yet been considered. This is in stark contrast with quantum computation proposals for Abelian anyons, for which decoding algorithms have been tailor-made for many topological error-correcting codes and error models. Here, we address this issue by considering the properties of non-Abelian error correction, in general. We also choose a specific anyon model and error model to probe the problem in more detail. The anyon model is the charge submodel of D(S_{3}. This shares many properties with important models such as the Fibonacci anyons, making our method more generally applicable. The error model is a straightforward generalization of those used in the case of Abelian anyons for initial benchmarking of error correction methods. It is found that error correction is possible under a threshold value of 7% for the total probability of an error on each physical spin. This is remarkably comparable with the thresholds for Abelian models.
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.
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
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.
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.
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.
Learning from prescribing errors
Dean, B
2002-01-01
The importance of learning from medical error has recently received increasing emphasis. This paper focuses on prescribing errors and argues that, while learning from prescribing errors is a laudable goal, there are currently barriers that can prevent this occurring. Learning from errors can take place on an individual level, at a team level, and across an organisation. Barriers to learning from prescribing errors include the non-discovery of many prescribing errors, lack of feedback to th...
Energy Technology Data Exchange (ETDEWEB)
Sameshima, M; Ito, K; Iwabuchi, M
1972-01-01
In the slime mold, Dictyostelium discoideum, when the rate of protein synthesis was decreased by NaF, free 80-S ribosomes accumulated at the expense of polyribosomes, while 60-S and 40-S ribosomal subunits remained almost constant. The same level of ribosomal subunits was also maintained in cells after incubation with cycloheximide or at the stationary phase of growth.
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.
Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome.
Greber, Basil J; Bieri, Philipp; Leibundgut, Marc; Leitner, Alexander; Aebersold, Ruedi; Boehringer, Daniel; Ban, Nenad
2015-04-17
Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of the porcine 55S mitoribosome at 3.8 angstrom resolution by cryo-electron microscopy and chemical cross-linking/mass spectrometry. The structure of the 28S subunit in the complex was resolved at 3.6 angstrom resolution by focused alignment, which allowed building of a detailed atomic structure including all of its 15 mitoribosomal-specific proteins. The structure reveals the intersubunit contacts in the 55S mitoribosome, the molecular architecture of the mitoribosomal messenger RNA (mRNA) binding channel and its interaction with transfer RNAs, and provides insight into the highly specialized mechanism of mRNA recruitment to the 28S subunit. Furthermore, the structure contributes to a mechanistic understanding of aminoglycoside ototoxicity. Copyright © 2015, American Association for the Advancement of Science.
Ribosomes slide on lysine-encoding homopolymeric A stretches
Koutmou, Kristin S; Schuller, Anthony P; Brunelle, Julie L; Radhakrishnan, Aditya; Djuranovic, Sergej; Green, Rachel
2015-01-01
Protein output from synonymous codons is thought to be equivalent if appropriate tRNAs are sufficiently abundant. Here we show that mRNAs encoding iterated lysine codons, AAA or AAG, differentially impact protein synthesis: insertion of iterated AAA codons into an ORF diminishes protein expression more than insertion of synonymous AAG codons. Kinetic studies in E. coli reveal that differential protein production results from pausing on consecutive AAA-lysines followed by ribosome sliding on homopolymeric A sequence. Translation in a cell-free expression system demonstrates that diminished output from AAA-codon-containing reporters results from premature translation termination on out of frame stop codons following ribosome sliding. In eukaryotes, these premature termination events target the mRNAs for Nonsense-Mediated-Decay (NMD). The finding that ribosomes slide on homopolymeric A sequences explains bioinformatic analyses indicating that consecutive AAA codons are under-represented in gene-coding sequences. Ribosome ‘sliding’ represents an unexpected type of ribosome movement possible during translation. DOI: http://dx.doi.org/10.7554/eLife.05534.001 PMID:25695637
The Phosphorylation of Ribosomal Protein in Lemna minor
Trewavas, A.
1973-01-01
Sterile cultures of Lemna minor have been labeled with 32P1, and the ribosomal proteins have been examined for radioactivity. In relatively short term labeling a radioactive protein was found which ran as a single component in both urea/acetic acid and sodium lauryl sulfate gel electrophoresis. Acid hydrolysis of the labeled protein permitted the isolation of serine phosphate. After labeling to equilibrium with 32P1, calculation indicated only 0.6 to 0.75 atom of this protein phosphorus per ribosome. The phosphorylated protein is found in both polysomes and “derived” monomers and appears to be located in the ribosomal small subunit. Its apparent molecular weight is 42,000. Addition of growth-inhibiting concentrations of abscisic acid does not alter the apparent degree of labeling of this protein in 5 hours, but after 24 hours of treatment the total protein phosphorus was reduced from 0.75 atom of phosphorus per ribosome to 0.36 atom of phosphorus per ribosome. PMID:16658405
Directory of Open Access Journals (Sweden)
Vingron Martin
2008-10-01
Full Text Available Abstract Background More than two thirds of the highly expressed ribosomal protein (RP genes in Saccharomyces cerevisiae contain introns, which is in sharp contrast to the genome-wide five percent intron-containing genes. It is well established that introns carry regulatory sequences and that the transcription of RP genes is extensively and coordinately regulated. Here we test the hypotheses that introns are innately associated with heavily transcribed genes and that introns of RP genes contribute regulatory TF binding sequences. Moreover, we investigate whether promoter features are significantly different between intron-containing and intronless RP genes. Results We find that directly measured transcription rates tend to be lower for intron-containing compared to intronless RP genes. We do not observe any specifically enriched sequence motifs in the introns of RP genes other than those of the branch point and the two splice sites. Comparing the promoters of intron-containing and intronless RP genes, we detect differences in number and position of Rap1-binding and IFHL motifs. Moreover, the analysis of the length distribution and the folding free energies suggest that, at least in a sub-population of RP genes, the 5' untranslated sequences are optimized for regulatory function. Conclusion Our results argue against the direct involvement of introns in the regulation of transcription of highly expressed genes. Moreover, systematic differences in motif distributions suggest that RP transcription factors may act differently on intron-containing and intronless gene promoters. Thus, our findings contribute to the decoding of the RP promoter architecture and may fuel the discussion on the evolution of introns.
Astrand, Elaine
2018-06-01
Working memory (WM), crucial for successful behavioral performance in most of our everyday activities, holds a central role in goal-directed behavior. As task demands increase, inducing higher WM load, maintaining successful behavioral performance requires the brain to work at the higher end of its capacity. Because it is depending on both external and internal factors, individual WM load likely varies in a continuous fashion. The feasibility to extract such a continuous measure in time that correlates to behavioral performance during a working memory task remains unsolved. Multivariate pattern decoding was used to test whether a decoder constructed from two discrete levels of WM load can generalize to produce a continuous measure that predicts task performance. Specifically, a linear regression with L2-regularization was chosen with input features from EEG oscillatory activity recorded from healthy participants while performing the n-back task, [Formula: see text]. The feasibility to extract a continuous time-resolved measure that correlates positively to trial-by-trial working memory task performance is demonstrated (r = 0.47, p performance before action (r = 0.49, p < 0.05). We show that the extracted continuous measure enables to study the temporal dynamics of the complex activation pattern of WM encoding during the n-back task. Specifically, temporally precise contributions of different spectral features are observed which extends previous findings of traditional univariate approaches. These results constitute an important contribution towards a wide range of applications in the field of cognitive brain-machine interfaces. Monitoring mental processes related to attention and WM load to reduce the risk of committing errors in high-risk environments could potentially prevent many devastating consequences or using the continuous measure as neurofeedback opens up new possibilities to develop novel rehabilitation techniques for
International Nuclear Information System (INIS)
Anon.
1991-01-01
This chapter addresses the extension of previous work in one-dimensional (linear) error theory to two-dimensional error analysis. The topics of the chapter include the definition of two-dimensional error, the probability ellipse, the probability circle, elliptical (circular) error evaluation, the application to position accuracy, and the use of control systems (points) in measurements
International Nuclear Information System (INIS)
Picard, R.R.
1989-01-01
Topics covered in this chapter include a discussion of exact results as related to nuclear materials management and accounting in nuclear facilities; propagation of error for a single measured value; propagation of error for several measured values; error propagation for materials balances; and an application of error propagation to an example of uranium hexafluoride conversion process
Martínez-Legaz, Juan Enrique; Soubeyran, Antoine
2003-01-01
We present a model of learning in which agents learn from errors. If an action turns out to be an error, the agent rejects not only that action but also neighboring actions. We find that, keeping memory of his errors, under mild assumptions an acceptable solution is asymptotically reached. Moreover, one can take advantage of big errors for a faster learning.
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.
Generalized Gaussian Error Calculus
Grabe, Michael
2010-01-01
For the first time in 200 years Generalized Gaussian Error Calculus addresses a rigorous, complete and self-consistent revision of the Gaussian error calculus. Since experimentalists realized that measurements in general are burdened by unknown systematic errors, the classical, widespread used evaluation procedures scrutinizing the consequences of random errors alone turned out to be obsolete. As a matter of course, the error calculus to-be, treating random and unknown systematic errors side by side, should ensure the consistency and traceability of physical units, physical constants and physical quantities at large. The generalized Gaussian error calculus considers unknown systematic errors to spawn biased estimators. Beyond, random errors are asked to conform to the idea of what the author calls well-defined measuring conditions. The approach features the properties of a building kit: any overall uncertainty turns out to be the sum of a contribution due to random errors, to be taken from a confidence inter...
Decoding thalamic afferent input using microcircuit spiking activity.
Sederberg, Audrey J; Palmer, Stephanie E; MacLean, Jason N
2015-04-01
A behavioral response appropriate to a sensory stimulus depends on the collective activity of thousands of interconnected neurons. The majority of cortical connections arise from neighboring neurons, and thus understanding the cortical code requires characterizing information representation at the scale of the cortical microcircuit. Using two-photon calcium imaging, we densely sampled the thalamically evoked response of hundreds of neurons spanning multiple layers and columns in thalamocortical slices of mouse somatosensory cortex. We then used a biologically plausible decoder to characterize the representation of two distinct thalamic inputs, at the level of the microcircuit, to reveal those aspects of the activity pattern that are likely relevant to downstream neurons. Our data suggest a sparse code, distributed across lamina, in which a small population of cells carries stimulus-relevant information. Furthermore, we find that, within this subset of neurons, decoder performance improves when noise correlations are taken into account. Copyright © 2015 the American Physiological Society.
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.
DECODING OF ACADEMIC CONTENT BY THE 1st GRADE STUDENTS
Directory of Open Access Journals (Sweden)
Kamil Błaszczyński
2017-07-01
Full Text Available In the paper a comparative study conducted on the 1st grade students of sociology and pedagogy is discussed. The study was focused on the language skills of students. The most important skills tested were the abilities to decode academic content. The study shows that the students have very poor language skills in decoding the academic content on every level of its complexity. They also have noticeable problems with the definition of basic academic terms. The significance of the obtained results are high because of the innovative topic and character of the study, which was the first such study conducted on students of a Polish university. Results are also valuable for academic teachers who are interested in such problems as effective communication with students.
Decoding Signal Processing at the Single-Cell Level
Energy Technology Data Exchange (ETDEWEB)
Wiley, H. Steven
2017-12-01
The ability of cells to detect and decode information about their extracellular environment is critical to generating an appropriate response. In multicellular organisms, cells must decode dozens of signals from their neighbors and extracellular matrix to maintain tissue homeostasis while still responding to environmental stressors. How cells detect and process information from their surroundings through a surprisingly limited number of signal transduction pathways is one of the most important question in biology. Despite many decades of research, many of the fundamental principles that underlie cell signal processing remain obscure. However, in this issue of Cell Systems, Gillies et al present compelling evidence that the early response gene circuit can act as a linear signal integrator, thus providing significant insight into how cells handle fluctuating signals and noise in their environment.
Reaction Decoder Tool (RDT): extracting features from chemical reactions.
Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M
2016-07-01
Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.
Fast decoder for local quantum codes using Groebner basis
Haah, Jeongwan
2013-03-01
Based on arXiv:1204.1063. A local translation-invariant quantum code has a description in terms of Laurent polynomials. As an application of this observation, we present a fast decoding algorithm for translation-invariant local quantum codes in any spatial dimensions using the straightforward division algorithm for multivariate polynomials. The running time is O (n log n) on average, or O (n2 log n) on worst cases, where n is the number of physical qubits. The algorithm improves a subroutine of the renormalization-group decoder by Bravyi and Haah (arXiv:1112.3252) in the translation-invariant case. This work is supported in part by the Insitute for Quantum Information and Matter, an NSF Physics Frontier Center, and the Korea Foundation for Advanced Studies.
Iterative decoding of SOVA and LDPC product code for bit-patterned media recoding
Jeong, Seongkwon; Lee, Jaejin
2018-05-01
The demand for high-density storage systems has increased due to the exponential growth of data. Bit-patterned media recording (BPMR) is one of the promising technologies to achieve the density of 1Tbit/in2 and higher. To increase the areal density in BPMR, the spacing between islands needs to be reduced, yet this aggravates inter-symbol interference and inter-track interference and degrades the bit error rate performance. In this paper, we propose a decision feedback scheme using low-density parity check (LDPC) product code for BPMR. This scheme can improve the decoding performance using an iterative approach with extrinsic information and log-likelihood ratio value between iterative soft output Viterbi algorithm and LDPC product code. Simulation results show that the proposed LDPC product code can offer 1.8dB and 2.3dB gains over the one LDPC code at the density of 2.5 and 3 Tb/in2, respectively, when bit error rate is 10-6.
45 Gb/s low complexity optical front-end for soft-decision LDPC decoders.
Sakib, Meer Nazmus; Moayedi, Monireh; Gross, Warren J; Liboiron-Ladouceur, Odile
2012-07-30
In this paper a low complexity and energy efficient 45 Gb/s soft-decision optical front-end to be used with soft-decision low-density parity-check (LDPC) decoders is demonstrated. The results show that the optical front-end exhibits a net coding gain of 7.06 and 9.62 dB for post forward error correction bit error rate of 10(-7) and 10(-12) for long block length LDPC(32768,26803) code. The performance over a hard decision front-end is 1.9 dB for this code. It is shown that the soft-decision circuit can also be used as a 2-bit flash type analog-to-digital converter (ADC), in conjunction with equalization schemes. At bit rate of 15 Gb/s using RS(255,239), LDPC(672,336), (672, 504), (672, 588), and (1440, 1344) used with a 6-tap finite impulse response (FIR) equalizer will result in optical power savings of 3, 5, 7, 9.5 and 10.5 dB, respectively. The 2-bit flash ADC consumes only 2.71 W at 32 GSamples/s. At 45 GSamples/s the power consumption is estimated to be 4.95 W.
Design and Implementation of Convolutional Encoder and Viterbi Decoder Using FPGA.
Directory of Open Access Journals (Sweden)
Riham Ali Zbaid
2018-01-01
Full Text Available Keeping the fineness of data is the most significant thing in communication.There are many factors that affect the accuracy of the data when it is transmitted over the communication channel such as noise etc. to overcome these effects are encoding channels encryption.In this paper is used for one type of channel coding is convolutional codes. Convolution encoding is a Forward Error Correction (FEC method used in incessant one-way and real time communication links .It can offer a great development in the error bit rates so that small, low energy, and devices cheap transmission when used in applications such as satellites. In this paper highlight the design, simulation and implementation of convolution encoder and Viterbi decoder by using MATLAB- program (2011. SIMULINK HDL coder is used to convert MATLAB-SIMULINK models to VHDL using plates Altera Cyclone II code DE2-70. Simulation and evaluation of the implementation of the results coincided with the results of the design show the coinciding with the designed results.
Label-Free Quantitation of Ribosomal Proteins from Bacillus subtilis for Antibiotic Research.
Schäkermann, Sina; Prochnow, Pascal; Bandow, Julia E
2017-01-01
Current research is focusing on ribosome heterogeneity as a response to changing environmental conditions and stresses, such as antibiotic stress. Altered stoichiometry and composition of ribosomal proteins as well as association of additional protein factors are mechanisms for shaping the protein expression profile or hibernating ribosomes. Here, we present a method for the isolation of ribosomes to analyze antibiotic-induced changes in the composition of ribosomes in Bacillus subtilis or other bacteria. Ribosomes and associated proteins are isolated by ultracentrifugation and proteins are identified and quantified using label-free mass spectrometry.
Medication errors: prescribing faults and prescription errors.
Velo, Giampaolo P; Minuz, Pietro
2009-06-01
1. Medication errors are common in general practice and in hospitals. Both errors in the act of writing (prescription errors) and prescribing faults due to erroneous medical decisions can result in harm to patients. 2. Any step in the prescribing process can generate errors. Slips, lapses, or mistakes are sources of errors, as in unintended omissions in the transcription of drugs. Faults in dose selection, omitted transcription, and poor handwriting are common. 3. Inadequate knowledge or competence and incomplete information about clinical characteristics and previous treatment of individual patients can result in prescribing faults, including the use of potentially inappropriate medications. 4. An unsafe working environment, complex or undefined procedures, and inadequate communication among health-care personnel, particularly between doctors and nurses, have been identified as important underlying factors that contribute to prescription errors and prescribing faults. 5. Active interventions aimed at reducing prescription errors and prescribing faults are strongly recommended. These should be focused on the education and training of prescribers and the use of on-line aids. The complexity of the prescribing procedure should be reduced by introducing automated systems or uniform prescribing charts, in order to avoid transcription and omission errors. Feedback control systems and immediate review of prescriptions, which can be performed with the assistance of a hospital pharmacist, are also helpful. Audits should be performed periodically.
DEFF Research Database (Denmark)
Greber, Basil J; Boehringer, Daniel; Godinic-Mikulcic, Vlatka
2012-01-01
additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter...... between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes......, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea....
Interaction of tRNA with Eukaryotic Ribosome
Directory of Open Access Journals (Sweden)
Dmitri Graifer
2015-03-01
Full Text Available This paper is a review of currently available data concerning interactions of tRNAs with the eukaryotic ribosome at various stages of translation. These data include the results obtained by means of cryo-electron microscopy and X-ray crystallography applied to various model ribosomal complexes, site-directed cross-linking with the use of tRNA derivatives bearing chemically or photochemically reactive groups in the CCA-terminal fragment and chemical probing of 28S rRNA in the region of the peptidyl transferase center. Similarities and differences in the interactions of tRNAs with prokaryotic and eukaryotic ribosomes are discussed with concomitant consideration of the extent of resemblance between molecular mechanisms of translation in eukaryotes and bacteria.
5SRNAdb: an information resource for 5S ribosomal RNAs.
Szymanski, Maciej; Zielezinski, Andrzej; Barciszewski, Jan; Erdmann, Volker A; Karlowski, Wojciech M
2016-01-04
Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA-protein interactions and molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across three domains of life. Here, we give an overview of new developments in the database and associated web tools since 2002, including updates to database content, curation processes and user web interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.
Structural basis for precursor protein-directed ribosomal peptide macrocyclization
Li, Kunhua; Condurso, Heather L.; Li, Gengnan; Ding, Yousong; Bruner, Steven D.
2016-01-01
Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides whose members target proteases with potent reversible inhibition. The product structure is constructed by three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here, we describe the detailed structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases, MdnC and MdnB, interact with a conserved α-helix of the precursor peptide using a novel precursor peptide recognition mechanism. The results provide insight into the unique protein/protein interactions key to the chemistry, suggest an origin of the natural combinatorial synthesis of microviridin peptides and provide a framework for future engineering efforts to generate designed compounds. PMID:27669417
Structural basis for precursor protein-directed ribosomal peptide macrocyclization.
Li, Kunhua; Condurso, Heather L; Li, Gengnan; Ding, Yousong; Bruner, Steven D
2016-11-01
Macrocyclization is a common feature of natural product biosynthetic pathways including the diverse family of ribosomal peptides. Microviridins are architecturally complex cyanobacterial ribosomal peptides that target proteases with potent reversible inhibition. The product structure is constructed via three macrocyclizations catalyzed sequentially by two members of the ATP-grasp family, a unique strategy for ribosomal peptide macrocyclization. Here we describe in detail the structural basis for the enzyme-catalyzed macrocyclizations in the microviridin J pathway of Microcystis aeruginosa. The macrocyclases MdnC and MdnB interact with a conserved α-helix of the precursor peptide using a novel precursor-peptide recognition mechanism. The results provide insight into the unique protein-protein interactions that are key to the chemistry, suggest an origin for the natural combinatorial synthesis of microviridin peptides, and provide a framework for future engineering efforts to generate designed compounds.
Iterative demodulation and decoding of coded non-square QAM
Li, L.; Divsalar, D.; Dolinar, S.
2003-01-01
Simulation results show that, with iterative demodulation and decoding, coded NS-8QAM performs 0.5 dB better than standard 8QAM and 0.7 dB better than 8PSK at BER= 10(sup -5), when the FEC code is the (15, 11) Hamming code concatenated with a rate-1 accumulator code, while coded NS-32QAM performs 0.25 dB better than standard 32QAM.
Design and Implementation of Viterbi Decoder Using VHDL
Thakur, Akash; Chattopadhyay, Manju K.
2018-03-01
A digital design conversion of Viterbi decoder for ½ rate convolutional encoder with constraint length k = 3 is presented in this paper. The design is coded with the help of VHDL, simulated and synthesized using XILINX ISE 14.7. Synthesis results show a maximum frequency of operation for the design is 100.725 MHz. The requirement of memory is less as compared to conventional method.
Decoding Gimmicks of Financial Shenanigans in Telecom Sector in India
Sandeep GOEL
2013-01-01
Major corporate financial shenanigans get away in the name of creative accounting. But, they need to be studied for lessons learned and strategies to avoid or reduce the incidence of such frauds in the future. It is essential for shareholders, particularly the common man who does not have any access to the company except reported financial numbers. This paper aims to decode the level of financial shenanigans practices in corporate enterprises in telecom sector in India. The reason being is th...
Protein-protein interactions within late pre-40S ribosomes.
Directory of Open Access Journals (Sweden)
Melody G Campbell
2011-01-01
Full Text Available Ribosome assembly in eukaryotic organisms requires more than 200 assembly factors to facilitate and coordinate rRNA transcription, processing, and folding with the binding of the ribosomal proteins. Many of these assembly factors bind and dissociate at defined times giving rise to discrete assembly intermediates, some of which have been partially characterized with regards to their protein and RNA composition. Here, we have analyzed the protein-protein interactions between the seven assembly factors bound to late cytoplasmic pre-40S ribosomes using recombinant proteins in binding assays. Our data show that these factors form two modules: one comprising Enp1 and the export adaptor Ltv1 near the beak structure, and the second comprising the kinase Rio2, the nuclease Nob1, and a regulatory RNA binding protein Dim2/Pno1 on the front of the head. The GTPase-like Tsr1 and the universally conserved methylase Dim1 are also peripherally connected to this second module. Additionally, in an effort to further define the locations for these essential proteins, we have analyzed the interactions between these assembly factors and six ribosomal proteins: Rps0, Rps3, Rps5, Rps14, Rps15 and Rps29. Together, these results and previous RNA-protein crosslinking data allow us to propose a model for the binding sites of these seven assembly factors. Furthermore, our data show that the essential kinase Rio2 is located at the center of the pre-ribosomal particle and interacts, directly or indirectly, with every other assembly factor, as well as three ribosomal proteins required for cytoplasmic 40S maturation. These data suggest that Rio2 could play a central role in regulating cytoplasmic maturation steps.
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
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.
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.
A streamlined ribosome profiling protocol for the characterization of microorganisms
DEFF Research Database (Denmark)
Latif, Haythem; Szubin, Richard; Tan, Justin
2015-01-01
Ribosome profiling is a powerful tool for characterizing in vivo protein translation at the genome scale, with multiple applications ranging from detailed molecular mechanisms to systems-level predictive modeling. Though highly effective, this intricate technique has yet to become widely used...... in the microbial research community. Here we present a streamlined ribosome profiling protocol with reduced barriers to entry for microbial characterization studies. Our approach provides simplified alternatives during harvest, lysis, and recovery of monosomes and also eliminates several time-consuming steps...
Interaction of pleuromutilin derivatives with the ribosomal peptidyl transferase center
DEFF Research Database (Denmark)
Long, K. S.; Hansen, L. K.; Jakobsen, L.
2006-01-01
Tiamulin is a pleuromutilin antibiotic that is used in veterinary medicine. The recently published crystal structure of a tiamulin-50S ribosomal subunit complex provides detailed information about how this drug targets the peptidyl transferase center of the ribosome. To promote rational design...... mutant strain is resistant to tiamulin and pleuromutilin, but not valnemulin, implying that valnemulin is better able to withstand an altered rRNA binding surface around the mutilin core. This is likely due to additional interactions made between the valnemulin side chain extension and the rRNA binding...
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.
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.
Fedyukina, Daria V.; Jennaro, Theodore S.; Cavagnero, Silvia
2014-01-01
Ribosomes are large and highly charged macromolecular complexes consisting of RNA and proteins. Here, we address the electrostatic and nonpolar properties of ribosomal proteins that are important for ribosome assembly and interaction with other cellular components and may influence protein folding on the ribosome. We examined 50 S ribosomal subunits from 10 species and found a clear distinction between the net charge of ribosomal proteins from halophilic and non-halophilic organisms. We found that ∼67% ribosomal proteins from halophiles are negatively charged, whereas only up to ∼15% of ribosomal proteins from non-halophiles share this property. Conversely, hydrophobicity tends to be lower for ribosomal proteins from halophiles than for the corresponding proteins from non-halophiles. Importantly, the surface electrostatic potential of ribosomal proteins from all organisms, especially halophiles, has distinct positive and negative regions across all the examined species. Positively and negatively charged residues of ribosomal proteins tend to be clustered in buried and solvent-exposed regions, respectively. Hence, the majority of ribosomal proteins is characterized by a significant degree of intramolecular charge segregation, regardless of the organism of origin. This key property enables the ribosome to accommodate proteins within its complex scaffold regardless of their overall net charge. PMID:24398678
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.
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...
Energy Technology Data Exchange (ETDEWEB)
Elliott, C.J.; McVey, B. (Los Alamos National Lab., NM (USA)); Quimby, D.C. (Spectra Technology, Inc., Bellevue, WA (USA))
1990-01-01
The level of field errors in an FEL is an important determinant of its performance. We have computed 3D performance of a large laser subsystem subjected to field errors of various types. These calculations have been guided by simple models such as SWOOP. The technique of choice is utilization of the FELEX free electron laser code that now possesses extensive engineering capabilities. Modeling includes the ability to establish tolerances of various types: fast and slow scale field bowing, field error level, beam position monitor error level, gap errors, defocusing errors, energy slew, displacement and pointing errors. Many effects of these errors on relative gain and relative power extraction are displayed and are the essential elements of determining an error budget. The random errors also depend on the particular random number seed used in the calculation. The simultaneous display of the performance versus error level of cases with multiple seeds illustrates the variations attributable to stochasticity of this model. All these errors are evaluated numerically for comprehensive engineering of the system. In particular, gap errors are found to place requirements beyond mechanical tolerances of {plus minus}25{mu}m, and amelioration of these may occur by a procedure utilizing direct measurement of the magnetic fields at assembly time. 4 refs., 12 figs.
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
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.
Multiple-Symbol Noncoherent Decoding of Uncoded and Convolutionally Codes Continous Phase Modulation
Divsalar, D.; Raphaeli, D.
2000-01-01
Recently, a method for combined noncoherent detection and decoding of trellis-codes (noncoherent coded modulation) has been proposed, which can practically approach the performance of coherent detection.
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.
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...
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.
Fault-tolerant quantum computing in the Pauli or Clifford frame with slow error diagnostics
Directory of Open Access Journals (Sweden)
Christopher Chamberland
2018-01-01
Full Text Available We consider the problem of fault-tolerant quantum computation in the presence of slow error diagnostics, either caused by measurement latencies or slow decoding algorithms. Our scheme offers a few improvements over previously existing solutions, for instance it does not require active error correction and results in a reduced error-correction overhead when error diagnostics is much slower than the gate time. In addition, we adapt our protocol to cases where the underlying error correction strategy chooses the optimal correction amongst all Clifford gates instead of the usual Pauli gates. The resulting Clifford frame protocol is of independent interest as it can increase error thresholds and could find applications in other areas of quantum computation.
Greber, Basil J.; Boehringer, Daniel; Godinic-Mikulcic, Vlatka; Crnkovic, Ana; Ibba, Michael; Weygand-Durasevic, Ivana; Ban, Nenad
2013-01-01
Translation of mRNA into proteins by the ribosome is universally conserved in all cellular life. The composition and complexity of the translation machinery differ markedly between the three domains of life. Organisms from the domain Archaea show an intermediate level of complexity, sharing several additional components of the translation machinery with eukaryotes that are absent in bacteria. One of these translation factors is initiation factor 6 (IF6), which associates with the large ribosomal subunit. We have reconstructed the 50S ribosomal subunit from the archaeon Methanothermobacter thermautotrophicus in complex with archaeal IF6 at 6.6 Å resolution using cryo-electron microscopy (EM). The structure provides detailed architectural insights into the 50S ribosomal subunit from a methanogenic archaeon through identification of the rRNA expansion segments and ribosomal proteins that are shared between this archaeal ribosome and eukaryotic ribosomes but are mostly absent in bacteria and in some archaeal lineages. Furthermore, the structure reveals that, in spite of highly divergent evolutionary trajectories of the ribosomal particle and the acquisition of novel functions of IF6 in eukaryotes, the molecular binding of IF6 on the ribosome is conserved between eukaryotes and archaea. The structure also provides a snapshot of the reductive evolution of the archaeal ribosome and offers new insights into the evolution of the translation system in archaea. PMID:22306461
Prescription Errors in Psychiatry
African Journals Online (AJOL)
Arun Kumar Agnihotri
clinical pharmacists in detecting errors before they have a (sometimes serious) clinical impact should not be underestimated. Research on medication error in mental health care is limited. .... participation in ward rounds and adverse drug.
Nuclear ribosomal DNA diversity of a cotton pest ( Rotylenchulus ...
African Journals Online (AJOL)
The reniform nematode (Rotylenchulus reniformis) has emerged as a major cotton pest in the United States. A recent analysis of over 20 amphimictic populations of this pest from the US and three other countries has shown no sequence variation at the nuclear ribosomal internal transcribed spacer (ITS) despite the region's ...