Build-up of auditory stream segregation induced by tone sequences of constant or alternating frequency and the resetting effects of single deviants

A sequence of constant-frequency tones can promote streaming in a subsequent sequence of alternating-frequency tones, but why this effect occurs is not fully understood and its time course has not been investigated. Experiment 1 used a 2.0-s-long constant-frequency inducer (10 repetitions of a low-frequency pure tone) to promote segregation in a subsequent, 1.2-s test sequence of alternating low- and high-frequency tones. Replacing the final inducer tone with silence substantially reduced reported test-sequence segregation. This reduction did not occur when either the 4th or 7th inducer was replaced with silence. This suggests that a change at the induction/test-sequence boundary actively resets build-up, rather than less segregation occurring simply because fewer inducer tones were presented. Furthermore, Experiment 2 found that a constant-frequency inducer produced its maximum segregation-promoting effect after only three tones—this contrasts with the more gradual build-up typically observed for alternating-frequency sequences. Experiment 3 required listeners to judge continuously the grouping of 20-s test sequences. Constant-frequency inducers were considerably more effective at promoting segregation than alternating ones; this difference persisted for ~10 s. In addition, resetting arising from a single deviant (longer tone) was associated only with constant-frequency inducers. Overall, the results suggest that constant-frequency inducers promote segregation by capturing one subset of test-sequence tones into an ongoing, preestablished stream, and that a deviant tone may reduce segregation by disrupting this capture. These findings offer new insight into the dynamics of stream segregation, and have implications for the neural basis of streaming and the role of attention in stream formation. (PsycINFO Database Record (c) 2013 APA, all rights reserved)

On the structural repertoire of pools of short, random RNA sequences

A detailed knowledge of the mapping between sequence and structure spaces in populations of RNA molecules is essential to better understand their present-day functional properties, to envisage a plausible early evolution of RNA in a prebiotic chemical environment and to improve the design of in vitro evolution experiments, among others. Analysis of natural RNAs, as well as in vitro and computational studies, show that certain RNA structural motifs are much more abundant than others, pointing out a complex relation between sequence and structure. Within this framework, we have investigated computationally the structural properties of a large pool (10 molecules) of single-stranded, 35 nt-long, random RNA sequences. The secondary structures obtained are ranked and classified into structure families. The number of structures in main families is analytically calculated and compared with the numerical results. This permits a quantification of the fraction of structure space covered by a large pool of sequences. We further show that the number of structural motifs and their frequency is highly unbalanced with respect to the nucleotide composition: simple structures such as stem-loops and hairpins arise from sequences depleted in G, while more complex structures require an enrichment of G. In general, we observe a strong correlation between subfamilies-characterized by a fixed number of paired nucleotides-and nucleotide composition. Our results are compared to the structural repertoire obtained in a second pool where isolated base pairs are prohibited. © 2008 Elsevier Ltd. All rights reserved.

TATPred:a Bayesian method for the identification of twin arginine translocation pathway signal sequences

The twin arginine translocation (TAT) system ferries folded proteins across the bacterial membrane. Proteins are directed into this system by the TAT signal peptide present at the amino terminus of the precursor protein, which contains the twin arginine residues that give the system its name. There are currently only two computational methods for the prediction of TAT translocated proteins from sequence. Both methods have limitations that make the creation of a new algorithm for TAT-translocated protein prediction desirable. We have developed TATPred, a new sequence-model method, based on a Nave-Bayesian network, for the prediction of TAT signal peptides. In this approach, a comprehensive range of models was tested to identify the most reliable and robust predictor. The best model comprised 12 residues: three residues prior to the twin arginines and the seven residues that follow them. We found a prediction sensitivity of 0.979 and a specificity of 0.942.

LIPPRED:a web server for accurate prediction of lipoprotein signal sequences and cleavage sites

Bacterial lipoproteins have many important functions and represent a class of possible vaccine candidates. The prediction of lipoproteins from sequence is thus an important task for computational vaccinology. Naïve-Bayesian networks were trained to identify SpaseII cleavage sites and their preceding signal sequences using a set of 199 distinct lipoprotein sequences. A comprehensive range of sequence models was used to identify the best model for lipoprotein signal sequences. The best performing sequence model was found to be 10-residues in length, including the conserved cysteine lipid attachment site and the nine residues prior to it. The sensitivity of prediction for LipPred was 0.979, while the specificity was 0.742. Here, we describe LipPred, a web server for lipoprotein prediction; available at the URL: http://www.jenner.ac.uk/LipPred/. LipPred is the most accurate method available for the detection of SpaseIIcleaved lipoprotein signal sequences and the prediction of their cleavage sites.

Build-up of auditory stream segregation induced by tone sequences of constant or alternating frequency and the resetting effects of single deviants

A sequence of constant-frequency tones can promote streaming in a subsequent sequence of alternating-frequency tones, but why this effect occurs is not fully understood and its time course has not been investigated. Experiment 1 used a 2.0-s-long constant-frequency inducer (10 repetitions of a low-frequency pure tone) to promote segregation in a subsequent, 1.2-s test sequence of alternating low- and high-frequency tones. Replacing the final inducer tone with silence substantially reduced reported test-sequence segregation. This reduction did not occur when either the 4th or 7th inducer was replaced with silence. This suggests that a change at the induction/test-sequence boundary actively resets build-up, rather than less segregation occurring simply because fewer inducer tones were presented. Furthermore, Experiment 2 found that a constant-frequency inducer produced its maximum segregation-promoting effect after only three tones—this contrasts with the more gradual build-up typically observed for alternating-frequency sequences. Experiment 3 required listeners to judge continuously the grouping of 20-s test sequences. Constant-frequency inducers were considerably more effective at promoting segregation than alternating ones; this difference persisted for ~10 s. In addition, resetting arising from a single deviant (longer tone) was associated only with constant-frequency inducers. Overall, the results suggest that constant-frequency inducers promote segregation by capturing one subset of test-sequence tones into an ongoing, preestablished stream, and that a deviant tone may reduce segregation by disrupting this capture. These findings offer new insight into the dynamics of stream segregation, and have implications for the neural basis of streaming and the role of attention in stream formation. (PsycINFO Database Record (c) 2013 APA, all rights reserved)

Representational difference analysis:Critical appraisal and method development for the identification of unique DNA sequences from prokaryotes

Representational difference analysis (RDA) has great potential for preferential amplification of unique but uncharacterised DNA sequences present in one source such as a whole genome, but absent from a related genome or other complex population of sequences. While a few examples of its successful exploitation have been published, the method has not been well dissected and robust, detailed published protocols are lacking. Here we examine the method in detail, suggest improvements and provide a protocol that has yielded key unique sequences from a pathogenic bacterial genome. © 2003 Elsevier Science B.V. All rights reserved.

On Averaging Null Sequences of Real-Valued Functions

If ξ is a countable ordinal and (fk) a sequence of real-valued functions we define the repeated averages of order ξ of (fk). By using a partition theorem of Nash-Williams for families of finite subsets of positive integers it is proved that if ξ is a countable ordinal then every sequence (fk) of real-valued functions has a subsequence (f'k) such that either every sequence of repeated averages of order ξ of (f'k) converges uniformly to zero or no sequence of repeated averages of order ξ of (f'k) converges uniformly to zero. By the aid of this result we obtain some results stronger than Mazur’s theorem.

Problems and Theorems in the Theory of Multiplier Sequences

The purpose of this paper is (1) to highlight some recent and heretofore unpublished results in the theory of multiplier sequences and (2) to survey some open problems in this area of research. For the sake of clarity of exposition, we have grouped the problems in three subsections, although several of the problems are interrelated. For the reader’s convenience, we have included the pertinent definitions, cited references and related results, and in several instances, elucidated the problems by examples.

Weakly Increasing Zero-Diminishing Sequences

The following problem, suggested by Laguerre’s Theorem (1884), remains open: Characterize all real sequences {μk} k=0...∞ which have the zero-diminishing property; that is, if k=0...n, p(x) = ∑(ak x^k) is any P real polynomial, then k=0...n, p(x) = ∑(μk ak x^k) has no more real zeros than p(x). In this paper this problem is solved under the additional assumption of a weak growth condition on the sequence {μk} k=0...∞, namely lim n→∞ | μn |^(1/n) < ∞. More precisely, it is established that the real sequence {μk} k≥0 is a weakly increasing zerodiminishing sequence if and only if there exists σ ∈ {+1,−1} and an entire function n≥1, Φ(z)= be^(az) ∏(1+ x/αn), a, b ∈ R^1, b =0, αn > 0 ∀n ≥ 1, ∑(1/αn) < ∞, such that µk = (σ^k)/Φ(k), ∀k ≥ 0.

Structural Analysis of Contours as the Sequences of the Digital Straight Segments and of the Digital Curve Arcs

Recognition of the object contours in the image as sequences of digital straight segments and/or digital curve arcs is considered in this article. The definitions of digital straight segments and of digital curve arcs are proposed. The methods and programs to recognize the object contours are represented. The algorithm to recognize the digital straight segments is formulated in terms of the growing pyramidal networks taking into account the conceptual model of memory and identification (Rabinovich [4]).

Build-up of auditory stream segregation induced by tone sequences of constant or alternating frequency and the resetting effects of single deviants

Three experiments investigated the dynamics of auditory stream segregation. Experiment 1 used a 2.0-s constant-frequency inducer (10 repetitions of a low-frequency pure tone) to promote segregation in a subsequent, 1.2-s test sequence of alternating low- and high-frequency tones. Replacing the final inducer tone with silence reduced reported test-sequence segregation substantially. This reduction did not occur when either the 4th or 7th inducer was replaced with silence. This suggests that a change at the induction/test-sequence boundary actively resets buildup, rather than less segregation occurring simply because fewer inducer tones were presented. Furthermore, Experiment 2 found that a constant-frequency inducer produced its maximum segregation-promoting effect after only 3 tone cycles - this contrasts with the more gradual build-up typically observed for alternating sequences. Experiment 3 required listeners to judge continuously the grouping of 20-s test sequences. Constant-frequency inducers were considerably more effective at promoting segregation than alternating ones; this difference persisted for ∼10 s. In addition, resetting arising from a single deviant (longer tone) was associated only with constant-frequency inducers. Overall, the results suggest that constant-frequency inducers promote segregation by capturing one subset of test-sequence tones into an on-going, pre-established stream and that a deviant tone may reduce segregation by disrupting this capture. © 2013 Acoustical Society of America.

Analysis of foveation sequences in congenital nystagmus

Congenital nystagmus (CN) is an ocular-motor disorder that appears at birth or during the first few months of life; it is characterised by involuntary, conjugated, bilateral to and fro ocular oscillations. Pathogenesis of congenital nystagmus is still unknown. Eye movement recording allow to extract and analyse nystagmus main features such as shape, amplitude and frequency; depending on the morphology of the oscillations nystagmus can be classified in different categories (pendular, jerk, horizontal unidirectional, bidirectional). In general, CN patient show a considerable decrease of the visual acuity: image fixation on the retina is disturbed by nystagmus continuous oscillations; however, image stabilisation is still achieved during the short foveation periods in which eye velocity slows down while the target image is placed onto the fovea. Visual acuity was found to be mainly dependent on foveation periods duration, but cycle-to-cycle foveation repeatability and reduction of retinal image velocities also contribute in increasing visual acuity. This study concentrate on cycle-to-cycle image position variation onto fovea, trying to characterise the sequences of foveation positions. Eye-movement (infrared oculographic or electro oculographic) recordings, relative to different gaze positions and belonging to more than 30 CN patients, were analysed. Preliminary results suggest that sequences of foveations show a cyclic pattern with a dominant frequency (around 0.3 Hz on average) much lower than that of the nystagmus (about 3.3 Hz on average). Sequences of foveations reveals an horizontal ocular swing of more than 2 degree on average, which can explain the low visual acuity of the CN patient. Current CN therapies, pharmacological treatment or surgery of the ocular muscles, mainly aim to increase the patient's visual acuity. Hence, it is fundamental to have an objective parameter (expected visual acuity) for therapy planning. The information about sequences of foveations can improve estimation of patient visual acuity. © 2008 Springer-Verlag.

Detection of foveation windows and analysis of foveation sequences in congenital nystagmus

Congenital nystagmus (CN) is an ocular-motor disorder characterised by involuntary, conjugated ocular oscillations, that can arise since the first months of life. Pathogenesis of congenital nystagmus is still under investigation. In general, CN patients show a considerable decrease of their visual acuity: image fixation on the retina is disturbed by nystagmus continuous oscillations, mainly horizontal. However, image stabilisation is still achieved during the short periods in which eye velocity slows down while the target image is placed onto the fovea (called foveation intervals). To quantify the extent of nystagmus, eye movement recording are routinely employed, allowing physicians to extract and analyse nystagmus main features such as shape, amplitude and frequency. Using eye movement recording, it is also possible to compute estimated visual acuity predictors: analytical functions which estimates expected visual acuity using signal features such as foveation time and foveation position variability. Use of those functions add information to typical visual acuity measurement (e.g. Landolt C test) and could be a support for therapy planning or monitoring. This study focus on robust detection of CN patients' foveations. Specifically, it proposes a method to recognize the exact signal tracts in which a subject foveates, This paper also analyses foveation sequences. About 50 eyemovement recordings, either infrared-oculographic or electrooculographic, from different CN subjects were acquired. Results suggest that an exponential interpolation for the slow phases of nystagmus could improve foveation time computing and reduce influence of breaking saccades and data noise. Moreover a concise description of foveation sequence variability can be achieved using non-fitting splines. © 2009 Springer Berlin Heidelberg.

Sequences of Maximal Degree Vertices in Graphs

2000 Mathematics Subject Classification: 05C35.

Topic Segmentation: How Much Can We Do by Counting Words and Sequences of Words

In this paper, we present an innovative topic segmentation system based on a new informative similarity measure that takes into account word co-occurrence in order to avoid the accessibility to existing linguistic resources such as electronic dictionaries or lexico-semantic databases such as thesauri or ontology. Topic segmentation is the task of breaking documents into topically coherent multi-paragraph subparts. Topic segmentation has extensively been used in information retrieval and text summarization. In particular, our architecture proposes a language-independent topic segmentation system that solves three main problems evidenced by previous research: systems based uniquely on lexical repetition that show reliability problems, systems based on lexical cohesion using existing linguistic resources that are usually available only for dominating languages and as a consequence do not apply to less favored languages and finally systems that need previously existing harvesting training data. For that purpose, we only use statistics on words and sequences of words based on a set of texts. This solution provides a flexible solution that may narrow the gap between dominating languages and less favored languages thus allowing equivalent access to information.