Insertion Errors Research Articles

Finding errors in DNA sequences.

An algorithm is described that can detect certain errors within coding regions of DNA sequences. The algorithm is based on the idea that an insertion or deletion error within a coding sequence would interrupt the reading frame and cause the correct translation of a DNA sequence to require one or more frameshifts. If the coding sequence shows similarity to a known protein sequence then such errors can be detected by comparing the conceptual translations of DNA sequences in all six reading frames with every sequence in a protein sequence data base. We have incorporated these ideas into a computer program, called DETECT, that can serve as an aid to the experimentalist who is determining new DNA sequences so that obvious errors may be located and corrected. The program has been tested using raw experimental data and against sequences from the European Molecular Biology Laboratory data base, annotated as containing frameshifts. We have also tested it using unidentified open reading frames that flank known, annotated genes in the GenBank data base. Many potential errors are apparent and in some cases functions can be suggested for the "corrected" versions of these reading frames leading to the identification of new genes. As more sequences are determined the power of this method will increase substantially.

Regioirregular polypropene prepared with silica-supported titanium catalysts

Silica-supported titanium catalysts were prepared either by treatment of a silica-supported TiCl 4 with alkyl aluminium under very mild conditions or by supporting CpTiCl 3 on silica. These catlysts gave polypropylene with a high content of insertion errors mostly in blocks of 2,1-oriented propene units. From the copolymerization of propene with a small amount of ethylene, it was found that ethylene is incorporated in the copolymer next to the propene unit with 2,1-orientation.

Syndiospecific polymerization of styrene. II. Monocyclopentadienyltributoxy titanium/methylaluminoxane catalyst

AbstractSyndiospecific polymerization of styrene was catalyzed by monocyclopentadienyltributoxy titanium/methylaluminoxane [CpTi (OBu)3/MAO]. The atactic and syndiotactic polystyrenes were separated by extracting the former with refluxing 2‐butanone. The activity and syndiospecificity of the catalyst were affected by changes in catalyst concentration and composition, polymerization temperature, and monomer concentration. Extremely high activity of 5 × 107 g PS (mol Ti mol S h)−1 with 99% yield of the syndiotactic product were achieved. The concentration of active species, [C*], has been determined by radiolabeling. The amount of the syndiospecific and nonspecific catalytic species, [C] and [C] respectively, correspond to 79 and 13% of the CpTi(OBu)3. The rate constants of propagation for C and C at 45°C are 10.8 and 2.0 (M s)−1, respectively, the corresponding rate constants for chain transfer to MAO are 6.2 × 10−4 and 4.3 × 10−4s−1. There was no deactivation of the catalytic species during a batch polymerization. The rate constant of chain transfer with monomer is 6.7 × 10−2 (M s)−1; the spontaneous β‐hydride transfer rate constant is 4.7 × 10−2 s−1. The polymerization activity and stereospecificity of the catalyst are highest at 45°C, both decreasing with either higher or lower temperature. The stereoregular polymer have broad MW distributions, M̄w/M̄n = 2.8–5.7, and up to three crystalline modifications. The Tm of the s‐PS polymerized at 0–90°C decreased from 261.8 to 241°C indicating thermally activated monomer insertion errors. The styrene polymerization behaviors were essentially insensitive to the dielectric constant of the medium.

Molecular sequence accuracy and the analysis of protein coding regions.

Molecular sequences, like all experimental data, have finite error rates. The impact of errors on the information content of molecular sequence data is dependent on the analytic paradigm used to interpret the data. We studied the impact of nucleic acid sequence errors on the ability to align predicted amino acid sequences with the sequences of related proteins. We found that with a simultaneous translation and alignment algorithm, identification of sequence homologies is resilient to the introduction of random errors. Proteins with greater than 30% sequence identity can be reliably recognized even in the presence of 1% frameshifting (insertion or deletion) error rates and 5% base substitution rates. Incorporation of prior knowledge about the location and characteristics of errors improves tolerance to error of amino acid sequence alignments. Similarly, inclusion of prior knowledge of biased codon utilization by yeast (Saccharomyces cerevisiae) allows reliable detection of correct reading frames in yeast sequences even in the presence of 5% substitution and 1% frameshift errors.

A recurrent error propagation network speech recognition system

This paper describes a speaker-independent phoneme and word recognition system based on a recurrent error propagation network (REPN) trained on the TIMIT database. The REPN is a fully recurrent error propagation network trained by the propagation of the gradient signal backwards in time. A variation of the stochastic gradient descent procedure is used which updates the weights by an adaptive step size in the direction given by the sign of the gradient. Phonetic context is stored internal to the network and the outputs are estimates of the probability that a given frame is part of a segment labelled with a context-independent phonetic symbol. During recognition, a dynamic programming match is made to find the most probable string of symbols. The one pass algorithm is used for phoneme and word recognition. The phoneme recognition rate for all 61 TIMIT symbols is 70·0% correct (63·5% accuracy including insertion errors) and on a reduced 39-symbol set the recognition rate is 76·5% correct (69·8%). This compares favourably with the results of other methods, such as HMMs, on the same database [K. F. Lee & H. W. Hon 1989. IEEE Transactions on Acoustics, Speech and Signal Processing, 37, 1641–1648; S. E. Levinson, M. Y. Liberman, A. Ljolje & L. G. Miller 1989. Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing. Glasgow, pp. 441–444]. Analysis of the phoneme recognition results shows that information available from bigram and durational constraints is adequately handled within the network allowing for efficient parsing of the network output. For comparison, there is less computation involved in the resulting scheme than in a one-state-per-phoneme HMM system. This is demonstrated by applying the recognizer to the DARPA 1000-word resource management task. Parsing the network output to the word level with no grammar and no pruning can be carried out in faster than real time on a SUN 4 330 workstation.

Long-Term Survivorship Analysis of Cruciate-Sparing Versus Cruciate-Sacrificing Knee Prostheses Using Meniscal Bearings

A comprehensive, interchangeable, low-contact-stress, mobile-bearing knee prosthesis system was developed and used over a 12-year period with both cemented and cementless fixation. Individual components of the system included a bicruciate-retaining meniscal bearing, a posterior cruciate-retaining meniscal bearing, and a cruciate-sacrificing, rotating-platform tibial component mated to the same femoral and rotating patellar components. Survivorship analysis of each implant type was performed to identify specific failure modes and trends for long-term survival of the implants in a wide variety of primary knee arthroplasties. Clinically, there were 46 prostheses of the bicruciate type followed for up to 12 years, 57 prostheses of the posterior-cruciate type followed for up to six years, and 108 prostheses of the rotating-platform type followed for up to ten years. All knees in this study had rotating-bearing patellar prostheses. Cumulative survivorship analysis using an end point of implant revision or a poor knee score revealed a small early failure rate of each implant in the first three years, associated with technical positioning or undersizing errors. This study indicates a predictable long-term survival of both cruciate-retaining and cruciate-sacrificing mobile-bearing knee prostheses as well as rotating-bearing patellar prostheses when used in primary knee arthroplasties that minimized technical errors of insertion.

Figures of merit for assessing connected-word recognisers

This paper is concerned mainly with the choice of a figure of merit for representing the performance of connected-word recognisers when DP word-symbol sequence matching is used for the scoring. Properties of the DP scoring method are discussed. Experimental tests using data from the DARPA Resource Management Task confirm a prediction made from random number simulations that DP scoring overestimates substitution errors and underestimates insertion and deletion errors. As a result, the commonly used total error measure has a particularly large bias. The use of an alternative measure, percent correct, results in lower bias but ignores insertion errors. A new figure of merit, weighted total errors, takes all three kinds of errors into account and minimises bias. Finally, some more sophisticated figures of merit are discussed briefly.

The Gynaeseal diaphragm tampon

Medical Journal of AustraliaVolume 152, Issue 1 p. 52-53 Letter to the Editor The Gynaeseal diaphragm tampon John F. Cattanach DObstRCOG, John F. Cattanach DObstRCOG 68 Manningtree Road, Hawthorn, VIC, 3122Search for more papers by this author John F. Cattanach DObstRCOG, John F. Cattanach DObstRCOG 68 Manningtree Road, Hawthorn, VIC, 3122Search for more papers by this author First published: 01 January 1990 https://doi.org/10.5694/j.1326-5377.1990.tb124442.xCitations: 2AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article.Citing Literature Volume152, Issue1January 1990Pages 52-53 RelatedInformation

Nearest Neighbor Influences on DNA Polymerase Insertion Fidelity

The kinetics of forming all possible single base substitution errors are measured for Drosophila melanogaster DNA polymerase alpha and avian myeloblastosis virus reverse transcriptase. Seventeen sites along bacteriophage M13 DNA are investigated so that effects of nearest neighbor base stacking on misinsertion kinetics can be evaluated. Polymerase alpha appears to be more error prone than reverse transcriptase. Polymerase alpha forms transversion mispairs at rates comparable to transition mispairs with two exceptions; A.A and C.C are formed with significantly higher and lower efficiencies, respectively. Reverse transcriptase forms transversions with lower efficiencies than transitions, especially low being A.G, G.G, and C.C. For both enzymes, misinsertion frequencies vary typically by 10-fold for the same mispair in different locations. Misinsertion frequency can be expressed as a product of two components, one based on Km and the other on Vmax. DNA polymerase alpha appears to use primarily Km discrimination (100-5000-fold) to achieve insertion fidelity while reverse transcriptase shows a greater balance between Km and Vmax discrimination. Nearest-neighbor base stacking interactions appear to have opposite effects on the two discrimination components. The 5'-nearest neighbor influence on Km is greater for correct insertions than for incorrect, while the influence on Vmax is greater for the incorrect base. Target sites that have pyrimidine as the 5'-nearest neighbor to incoming nucleotides show a higher than average misinsertion component based on Km, but a lower than average component based on Vmax. Conversely, target sites with nearest neighbor purines have a higher than average Vmax component. These results imply that nucleotide misinsertion "hot spots" will occur next to pyrimidines when Km discrimination is dominant and next to purines when Vmax discrimination is dominant. When Vmax and Km discrimination components have similar magnitudes, nearest neighbor effects tend to cancel thereby reducing the effects of base stacking on insertion error rates.

Concept recognition: An approximate reasoning framework

This article presents a knowledge based methodology for recognizing concept instances in complex data such as natural scenes or speech signals. the architecture of a prototype system performing this task is also described. In order to obtain the capability of handling noisy patterns, the knowledge representation is based on continuous valued logics, and the inference engine is able to do sophisticated reasoning about the knowledge it uses in order to take into account the possible degradation of cues in the pattern. The knowledge base is subdivided into a bulk knowledge and a degradation theory. the bulk knowledge consists of production rules capturing discriminating cues in the signal as they appear in the normal cases. the degradation theory describes how the cues can be degraded owing to insertion and deletion errors. The whole classification process consists of two phases. First of all, the rules of the bulk knowledge are applied to the pattern, trying to obtain a suitable classification, and the evidence assigned to the rules is combined with a technique based on Dempster-Shafer theory. In the second phase, the classification is refined taking into account also the possible degradations in the pattern. the resulting system is then able to deal with different kinds of uncertainty and errors, such as fluctuation in the values measured for the pattern and insertion-deletion errors. the method is illustrated and evaluated on a simple example of spoken word recognition. (This work has been developed within the pilot project ESPRIT No. 26. © 1989 Wiley Periodicals, Inc.)

A method for selecting an optimum phoneme sequence using a posteriori probabilities of phonemes

A phoneme recognition system using phoneme discriminant filters was proposed, where segmentation and phoneme recognition were carried out simultaneously. However, the method had many phoneme insertion errors and often produced phoneme sequences that were inconsistent with Japanese phoneme connection rules. This paper proposes methods for reducing the number of phoneme insertion errors using inhibitory functions and for selecting an optimum phoneme sequence using dynamic programming based on the a posteriori probabilities of the phonemes. The definition of inhibitory functions is based on the Japanese phoneme connection rules and the phoneme duration information. This method was tested for the recognition of phonemes in a 212‐work vocabulary uttered by ten male speakers. The inhibitory functions reduced the total number of phoneme insertion errors to 1/5 and, especially, reduced the number of consonant insertion errors. The a posteriori probabilities of phonemes were computed based on distributions of the output of the phoneme discriminant filters.

Suboptimal, two-burn, midlevel thrust, LEO-GEO transfer mechanization and error analysis

This paper presents the results of additional work performed at INTELSAT in the area of LEO-GEO transfer. Previous work had produced an algorithm for the synthesis of two-burn, midlevel thrust, LEO-GEO transfer, the definition of the basic requirements of a constant rate steering law to approximate nominal trajectories and the simulation of trajectories. This paper presents the details of an attitude control system concept for the implementation of the constant rate steering law and an analysis of the effects of the control system errors. The control system mechanization is centered around a set of three, single-axis, strap-down, orthogonal rate-integrating gyros, and a processor for the storage of precomputed input commands and for the integrations required to reorient the vehicle prior to each burn. The error analysis, based on an INTELSAT VI application example, shows the GEO insertion errors resulting from the control system attitude errors at the beginning of each burn and from the rate errors.

Automatic text alignment for speech system evaluation

This paper describes an algorithm which automatically aligns two text strings, maximizing phoneme-to-phoneme similarities between strings, The alignment problem is formulated in an unconstrained endpoint dynamic optimization framework, and operates on phonemic transcriptions of input text strings. A modification of standard dynamic programming approach allows insertion and rejection errors in either string to be correctly identified. Benchmark evaluations show performance of algorithm approaches the expert speech scientist. The algorithm is an ideal tool for automated evaluation of experimental data, including data collected from speech intelligibility experiments and speech recognition experiments.

Operator product expansions in the massless Schwinger model

The known operator solution of the massless Schwinger model is used to calculate exactly, in three operator product expansions, the coefficient functions of the first few operators of low dimension which contribute when vacuum matrix elements are to be taken. A comparison of the results provides a test of the procedure used by M. A. Shifman, A. I. Vainshtein, and V. I. Zakharov [ Nucl. Phys. B 147 (1979), 385–447] in their study of QCD. It is found that the shift in vacua does not affect the calculation of coefficient functions. The vacuum insertion approximation yields somewhat misleading estimates of vacuum expectation values of some composite operators; however, the standard method used to estimate the errors of vacuum insertion indicates that the approximation is unreliable in this model.

Collection and characterization of spelling errors in scientific and scholarly text

AbstractThe SPEEDCOP (SPEIIing Error Detection correction Project) project recently completed at Chemical Abstracts Service (CAS) extracted over 50,000 misspellings from approximately 25,000,000 words of text from seven scientific and scholarly databases. The misspellings were automatically classified and the error types analyzed. The results, which were consistent over the different databases, showed that the expected incidence of misspelling is 0.2%, that 90–95% of spelling errors have only a single mistake, that substitution is homogeneous while transposition is heterogeneous, that omission is the commonest type of misspelling, and that inadvertent doubling of a letter is the most important cause of insertion errors. The more frequently a letter occurs in the text, the more likely it is to be involved in a spelling error. Most misspellings collected by SPEEDCOP are of the type colloquially referred to as “typos” and approximately 90% are unlikely to be repeated in normal spans of text.

An effective algorithm for string correction using generalized edit distances—I. Description of the algorithm and its optimality

This paper deals with the problem of estimating a transmitted string X s from the corresponding received string Y, which is a noisy version of X s . We assume that Y contains any number of substitution, insertion, and deletion errors, and that no two consecutive symbols of X s were deleted in transmission. We have shown that for channels which cause independent errors, and whose error probabilities exceed those of noisy strings studied in the literature [12], at least 99.5% of the erroneous strings will not contain two consecutive deletion errors. The best estimate X + of X s is defined as that element of H which minimizes the generalized Levenshtein distance D( X Y ) between X and Y. Using dynamic programming principles, an algorithm is presented which yields X + without computing individually the distances between every word of H and Y. Though this algorithm requires more memory, it can be shown that it is, in general, computationally less complex than all other existing algorithms which perform the same task.

LANGUAGE COMPETENCE AND READING STRATEGIES: A COMPARISON OF FIRST‐AND SECOND‐LANGUAGE ORAL READING ERRORS1

The French oral reading errors of two groups of seventh‐grade English‐speaking students with intermediate and advanced competence in French as a second language were analyzed and compared to the errors of native French‐speaking students. It was found that the intermediate students made a significantly lower proportion of deletion and insertion errors than did the advanced and nativespeaker students and a significantly higher proportion of substitution errors that graphically resembled the text than did the native speakers. Also, the intermediate students made a significantly higher proportion of errors that did not conform to the syntactic, semantic, or discourse constraints of the text than did the advanced and native‐speaker students. It was concluded that both native French‐speaking students and students with advanced competence in French as a second language appeared to use an interactive strategy of drawing on both graphic and contextual information in reading French. In contrast, students with less competence in French did not use contextual information to the same extent and instead employed a more “bottom‐up” strategy of relying primarily on graphic information.

Error-Correcting Parsers for Formal Languages

This paper describes error-correcting parsers for context-free and context-sensitive languages with substitution, insertion and deletion errors. Furthermore, it is shown that the ability of the proposed parsers can be expressed in terms of the weighted Levenshtein metric.

Stochastic Error-Correcting Syntax Analysis for Recognition of Noisy Patterns

In this paper, a probabilistic model for error-correcting parsing with substitution, insertion, and deletion errors is introduced. The formulation of maximum-likelihood error-correcting parser (MLECP) by incorporating the noise model into stochastic grammars is also presented. The use of stochastic error-correcting parsers for recognition of noisy and/or distorted patterns results in a process of high accuracy, but with low efficiency. In order to make the syntax analysis more practically feasible, it is proposed to use a sequential classification method for noisy strings processing. Computation results based on the classification experiments of noisy patterns for both nonsequential and sequential error-correcting parsers are presented.

A binary n-gram technique for automatic correction of substitution, deletion, insertion and reversal errors in words

A binary n-gram technique for automatic correction of substitution, deletion, insertion and reversal errors in words