Algorithmic computation of knot polynomials of secondary structure elements of proteins

The classification of protein structures is an important and still outstanding problem. The purpose of this paper is threefold. First, we utilize a relation between the Tutte and homfly polynomial to show that the Alexander-Conway polynomial can be algorithmically computed for a given planar graph. Second, as special cases of planar graphs, we use polymer graphs of protein structures. More precisely, we use three building blocks of the three-dimensional protein structure-alpha-helix, antiparallel beta-sheet, and parallel beta-sheet-and calculate, for their corresponding polymer graphs, the Tutte polynomials analytically by providing recurrence equations for all three secondary structure elements. Third, we present numerical results comparing the results from our analytical calculations with the numerical results of our algorithm-not only to test consistency, but also to demonstrate that all assigned polynomials are unique labels of the secondary structure elements. This paves the way for an automatic classification of protein structures.

Fast automatic two-stage nonlinear model identification based on the extreme learning machine

It is convenient and effective to solve nonlinear problems with a model that has a linear-in-the-parameters (LITP) structure. However, the nonlinear parameters (e.g. the width of Gaussian function) of each model term needs to be pre-determined either from expert experience or through exhaustive search. An alternative approach is to optimize them by a gradient-based technique (e.g. Newton’s method). Unfortunately, all of these methods still need a lot of computations. Recently, the extreme learning machine (ELM) has shown its advantages in terms of fast learning from data, but the sparsity of the constructed model cannot be guaranteed. This paper proposes a novel algorithm for automatic construction of a nonlinear system model based on the extreme learning machine. This is achieved by effectively integrating the ELM and leave-one-out (LOO) cross validation with our two-stage stepwise construction procedure [1]. The main objective is to improve the compactness and generalization capability of the model constructed by the ELM method. Numerical analysis shows that the proposed algorithm only involves about half of the computation of orthogonal least squares (OLS) based method. Simulation examples are included to confirm the efficacy and superiority of the proposed technique.

Tongue-tied?: An Active Analysis of Brian Friel's Translations

This article has arisen from a research-led production of Translations by Brian Friel for Queen’s University’s Tyrone Guthrie Society in February 2010. Drawing partly on a review of the existing critical literature and also from questions left unresolved by a previous experience of directing the play, the production sought to address through ‘active analysis’ (Merlin 2001) a number of research questions relating to the embodied nature of the rehearsal process and the historicity of Friel’s play. The analysis invokes Bergson (1910), Lefebvre (1991) and Worthern (2006) in establishing a performative correlative for insightful but more literary studies by Connolly (1993), Lojek (1994) and McGrath (1989 & 1999). A detailed account of the rehearsal process helps reveal the extent to which the idea of failure of communication is embedded in the text and embodied in performance, while an experiment with the partial use of the Irish language casts further light on Friel’s extraordinary device of rendering two languages through the medium of one. The use of music to counterpoint, rather than underscore the action, together with an achronological sequence of projected historical images inspired by Andrews (1983) provided me as director a means to challenge the audience’s presuppositions about the play. The sense of palimpsest, of the layered histories, that this evoked also served to highlight Friel’s use of the wider stylistic palette of Anglo-Irish drama, revealing Translations as a forerunner for Stewart Parker’s more explicit formal experiments in Northern Star. In rehearsal and performance Friel’s place in the continuum of the Irish theatrical canon became clear, as stylistic allusions to O’Casey, Shaw, Wilde and Beckett were embodied by the actors on the rehearsal room floor.

Dynamic evolution of the genetic search region through fuzzy coding

A technique for automatic exploration of the genetic search region through fuzzy coding (Sharma and Irwin, 2003) has been proposed. Fuzzy coding (FC) provides the value of a variable on the basis of the optimum number of selected fuzzy sets and their effectiveness in terms of degree-of-membership. It is an indirect encoding method and has been shown to perform better than other conventional binary, Gray and floating-point encoding methods. However, the static range of the membership functions is a major problem in fuzzy coding, resulting in longer times to arrive at an optimum solution in large or complicated search spaces. This paper proposes a new algorithm, called fuzzy coding with a dynamic range (FCDR), which dynamically allocates the range of the variables to evolve an effective search region, thereby achieving faster convergence. Results are presented for two benchmark optimisation problems, and also for a case study involving neural identification of a highly non-linear pH neutralisation process from experimental data. It is shown that dynamic exploration of the genetic search region is effective for parameter optimisation in problems where the search space is complicated.

Simple method for the rapid simultaneous screening of photocatalytic activity over multiple positions of self-cleaning films

An intelligent ink, previously shown to be capable of rapidly assessing photocatalytic activity, was simply applied via a felt-pen onto a commercially available piece of Activ (TM) self-cleaning glass. The ink, comprising of redox dye resazurin and the sacrificial electron donor glycerol within an aqueous hydroxy ethyl cellulose (HEC) polymer media, was photocatalytically degraded in a two-step process. The key initial stage was the photo-reductive conversion of resazurin to resorufin, whereby a colour change from blue to pink occurred. The latter stage was the subsequent photo-reduction of the resorufin, where a slower change from pink to colourless was seen. Red and green components of red-green-blue colour extracted from flat-bed scanner digital images of resazurin ink coated photocatalytic films at intervals during the photocatalysis reaction were inversely proportional to the changes seen via UV-visible absorption spectroscopy and indicative of reaction kinetics. A 3 x 3 grid of intelligent ink was drawn onto a piece of Activ (TM) and a glass blank. The photocatalysis reaction was monitored solely by flat-bed digital scanning. Red-green-blue values of respective positions on the grid were extracted using a custom-built program entitled RGB Extractor (c). The program was capable of extracting a number of 5 x 5 pixel averages of red-green-blue components simultaneously. Allocation of merely three coordinates allowed for the automatic generation of a grid, with scroll-bars controlling the number of positions to be extracted on the grid formed. No significant change in red and green components for any position on the glass blank was observed; however, the Activ (TM) film displayed a homogenous photo-reduction of the dye, reaching maxima in red and minima in green components in 23 +/- 3 and 14 +/- 2 min, respectively. A compositionally graded N-doped titania film synthesised in house via a combinatorial APCVD reaction was also photocatalytically tested by this method where 247 positions on a 13 x 19 grid were simultaneously analysed. The dramatic variation in photocatalysis observed was rapidly quantified for all positions (2-3 hours) allowing for correlations to be made between thicknesses and N : Ti% compositions attained from Swanepoel and WDX analysis, respectively. N incorporation within this system was found to be detrimental to film activity for the photocatalysis reaction of intelligent ink under 365 nm light.

The Paralax Infrastructure: Automatic Parallelization With a Helping Hand

Speeding up sequential programs on multicores is a challenging problem that is in urgent need of a solution. Automatic parallelization of irregular pointer-intensive codes, exempli?ed by the SPECint codes, is a very hard problem. This paper shows that, with a helping hand, such auto-parallelization is possible and fruitful. This paper makes the following contributions: (i) A compiler framework for extracting pipeline-like parallelism from outer program loops is presented. (ii) Using a light-weight programming model based on annotations, the programmer helps the compiler to ?nd thread-level parallelism. Each of the annotations speci?es only a small piece of semantic information that compiler analysis misses, e.g. stating that a variable is dead at a certain program point. The annotations are designed such that correctness is easily veri?ed. Furthermore, we present a tool for suggesting annotations to the programmer. (iii) The methodology is applied to autoparallelize several SPECint benchmarks. For the benchmark with most parallelism (hmmer), we obtain a scalable 7-fold speedup on an AMD quad-core dual processor. The annotations constitute a parallel programming model that relies extensively on a sequential program representation. Hereby, the complexity of debugging is not increased and it does not obscure the source code. These properties could prove valuable to increase the ef?ciency of parallel programming.

Semiotics, Presence and the Sublime in the Work of Alvin Lucier

Alvin Lucier, in his uncompromising exploration into the artistic potential of acoustic phenomena, has developed a body of work that remains highly original and hugely influential across many disciplines. His seminal works such as I am sitting in a room and Music for Solo Performer foreshadowed ways of approaching sound that are in common use among electro-acoustic composers, installation artists, as well as in commercial products. Lucier, despite his far reaching influence, is and has always been a composer, and his explorations of acoustics have been singularly focused on the development of a rich body of music. In this article, I investigate Lucier’s unique approach and attitude towards acoustics and aspire to enumerate important aesthetic developments he has made in creating music through the exploration of acoustic phenomena. In particular, this article seeks to investigate the role of semiotics in Lucier’s work, commenting on the pre-linguistic nature of Lucier’s approach to acoustic phenomenon. Here as well, an exploration of Lucier’s musical materials takes place, focusing on his instrumental compositions, specifically Diamonds for One, Two or Three Orchestras, where instruments are used as catalysts to generate in real-time acoustic phenomenon which interact to produce a rich yet intimate world of sound. Finally, Lucier’s approach to semiotics and real-time generation of music is viewed through a sublime aesthetic provoking questions regarding issues of presence and the now.

Temporal extension of Laplacian Eigenmaps for unsupervised dimensionality reduction of time series

A novel non-linear dimensionality reduction method, called Temporal Laplacian Eigenmaps, is introduced to process efficiently time series data. In this embedded-based approach, temporal information is intrinsic to the objective function, which produces description of low dimensional spaces with time coherence between data points. Since the proposed scheme also includes bidirectional mapping between data and embedded spaces and automatic tuning of key parameters, it offers the same benefits as mapping-based approaches. Experiments on a couple of computer vision applications demonstrate the superiority of the new approach to other dimensionality reduction method in term of accuracy. Moreover, its lower computational cost and generalisation abilities suggest it is scalable to larger datasets. © 2010 IEEE.

Multiple Luminaire Identification in Airborne Images of Airport’s Approach Lighting Using Mathematical Morphology With Variable Length Structuring Element

The increasing demand for fast air transportation around the clock
has increased the number of night flights in civil aviation over
the past few decades. In night aviation, to land an aircraft, a
pilot needs to be able to identify an airport. The approach
lighting system (ALS) at an airport is used to provide
identification and guidance to pilots from a distance. ALS
consists of more than $100$ luminaires which are installed in a
defined pattern following strict guidelines by the International
Civil Aviation Organization (ICAO). ICAO also has strict
regulations for maintaining the performance level of the
luminaires. However, once installed, to date there is no automated
technique by which to monitor the performance of the lighting. We
suggest using images of the lighting pattern captured using a camera
placed inside an aircraft. Based on the information contained
within these images, the performance of the luminaires has to be
evaluated which requires identification of over $100$ luminaires
within the pattern of ALS image. This research proposes analysis
of the pattern using morphology filters which use a variable
length structuring element (VLSE). The dimension of the VLSE changes
continuously within an image and varies for different images.
A novel
technique for automatic determination of the VLSE is proposed and
it allows successful identification of the luminaires from the
image data as verified through the use of simulated and real data.

Dis)Harmony in Illyria: Music, Order, and Time in Twelfth Night:Music, Order, and Time in Twelfth Night

This paper considers the integral aspect of music as performed in Shakespeare's Twelfth Night. It posits that music is that which orders and structures time in its interplay throughout the play.

Temporal guidance of musicians’ performance movement is an acquired skill

The ancillary (non-sounding) body movements made by expert musicians during performance have been shown to indicate expressive, emotional, and structural features of the music to observers, even if the sound of the performance is absent. If such ancillary body movements are a component of skilled musical performance, then it should follow that acquiring the temporal control of such movements is a feature of musical skill acquisition. This proposition is tested using measures derived from a theory of temporal guidance of movement, “General Tau Theory” (Lee in Ecol Psychol 10:221–250, 1998; Lee et al. in Exp Brain Res 139:151–159, 2001), to compare movements made during performances of intermediate-level clarinetists before and after learning a new piece of music. Results indicate that the temporal control of ancillary body movements made by participants was stronger in performances after the music had been learned and was closer to the measures of temporal control found for an expert musician’s movements. These findings provide evidence that the temporal control of musicians’ ancillary body movements develops with musical learning. These results have implications for other skillful behaviors and nonverbal communication.

Automaticity of cognitive biases in addictive behaviours: Further evidence with gamblers

Objectives. The hypotheses that automatic, non-volitional, attentional and memory biases for addiction-related constructs exist is tested with compulsive gamblers.

Design. An independent groups design was employed. Processing of gambling, compared to neutral and drug-related information was examined in 15 gamblers recruited from new members of Gamblers Anonymous. Comparisons were made with the performance of their spouses (N = 15) to help distinguish addiction mechanisms from more non-specific emotional experiences with gambling, and an independent control group (N = 15), recruited from the staff and students of a university department.

Methods. A modified Stroop procedure was first employed. Automative cognitive interference was assessed relatively, by comparing colour-naming times on the gambling, drug and neutral Stroops. A subsequent word-stem completion task of implicit memory was then used to assess selective and automatic priming of the gambling constructs in memory.

Results. Only the gamblers showed selective and automatic interference for gambling-related constructs on the Stroop task. Spouses behaved like the control group on this task. An implicit memory bias for gambling-related words was statistically detected only in the gamblers compared to the control group, although the trend was similar in the comparison with spouses. Further evidence for the specificity of these effects was obtained in subgroup comparisons involving fruit-machine with racing gamblers.

Conclusions. Results are generally consistent with an automaticity in the cognitive biases gamblers show for gambling-related information. implications for cognitive understanding and treatments are highlighted.

Oppositional Political Identity in the Song Culture of the Vormärz and the 1848 Revolution in Germany

Historically political song has often been perceived negatively, as a disturbance of the peace, summed up by the legendary line from Goethe’s Faust: “Politisches Lied – ein garstiges Lied”. In the period in Germany of the Vormärz (from 1815 up to the revolution of March 1848), however, we see how this perception may be changing as it increasingly becomes a means of self-expression in public life. This was the era of restauration, in which broader sections of German society are striving for political emancipation from the princes and kings. A whole host of political themes emerge in the songs (Freiheitslieder) of that period in which a new oppositional political consciousness is reflected. The themes range from freedom of speech, freedom from censorship, and the need for democratic and national self-determination to critiques of injustice and hunger, and parodies of political convention and opportunism. Sources of reception give indications about the social and political milieus in which these songs circulated. Such sources include broadsheets, handwritten manuscripts, song collections, commemoration events, advertisements in political press, memoires, police reports and general literature of the time. In many cases we see how these songs reflect the emerging social and political identities of those who sing them. One also sees the use of well known melodies in the popular dissemination of these songs. An intertextual function of music often becomes apparent in the practice of contrefacture whereby melodies with particular semantic associations are used to either underline the message or parody the subject of the song.

Xenopus cytoplasmic linker-associated protein 1 (XCLASP1) promotes axon elongation and advance of pioneer microtubules

Dynamic microtubules (MTs) are required for neuronal guidance, in which axons extend directionally toward their target tissues. We found that depletion of the MT-binding protein Xenopus cytoplasmic linker-associated protein 1 (XCLASP1) or treatment with the MT drug Taxol reduced axon outgrowth in spinal cord neurons. To quantify the dynamic distribution of MTs in axons, we developed an automated algorithm to detect and track MT plus ends that have been fluorescently labeled by end-binding protein 3 (EB3). XCLASP1 depletion reduced MT advance rates in neuronal growth cones, very much like treatment with Taxol, demonstrating a potential link between MT dynamics in the growth cone and axon extension. Automatic tracking of EB3 comets in different compartments revealed that MTs increasingly slowed as they passed from the axon shaft into the growth cone and filopodia. We used speckle microscopy to demonstrate that MTs experience retrograde flow at the leading edge. Microtubule advance in growth cone and filopodia was strongly reduced in XCLASP1-depleted axons as compared with control axons, but actin retrograde flow remained unchanged. Instead, we found that XCLASP1-depleted growth cones lacked lamellipodial actin organization characteristic of protrusion. Lamellipodial architecture depended on XCLASP1 and its capacity to associate with MTs, highlighting the importance of XCLASP1 in actin-microtubule interactions.