Modelling metrical flux: an adaptive frequency neural network for expressive rhythmic perception and prediction

Beat induction is the perceptual and cognitive process by which humans listen to music and perceive a steady pulse. Computationally modelling beat induction is important for many Music Information Retrieval (MIR) methods and is in general an open problem, especially when processing expressive timing, e.g. tempo changes or rubato. A neuro-cognitive model has been proposed, the Gradient Frequency Neural Network (GFNN), which can model the perception of pulse and metre. GFNNs have been applied successfully to a range of ‘difficult’ music perception problems such as polyrhythms and syncopation. This thesis explores the use of GFNNs for expressive rhythm perception and modelling, addressing the current gap in knowledge for how to deal with varying tempo and expressive timing in automated and interactive music systems. The cannonical oscillators contained in a GFNN have entrainment properties, allowing phase shifts and resulting in changes to the observed frequencies. This makes them good candidates for solving the expressive timing problem. It is found that modelling a metrical perception with GFNNs can improve a machine learning music model. However, it is also discovered that GFNNs perform poorly when dealing with tempo changes in the stimulus. Therefore, a novel Adaptive Frequency Neural Network (AFNN) is introduced; extending the GFNN with a Hebbian learning rule on oscillator frequencies. Two new adaptive behaviours (attraction and elasticity) increase entrainment in the oscillators, and increase the computational efficiency of the model by allowing for a great reduction in the size of the network. The AFNN is evaluated over a series of experiments on sets of symbolic and audio rhythms both from the literature and created specifically for this research. Where previous work with GFNNs has focused on frequency and amplitude responses, this thesis considers phase information as critical for pulse perception. Evaluating the time-based output, it was found that AFNNs behave differently to GFNNs: responses to symbolic stimuli with both steady and varying pulses are significantly improved, and on audio data the AFNNs performance matches the GFNN, despite its lower density. The thesis argues that AFNNs could replace the linear filtering methods commonly used in beat tracking and tempo estimation systems, and lead to more accurate methods

Generating Time: Rhythmic Perception, Prediction and Production with Recurrent Neural Networks

In the quest for a convincing musical agent that performs in real time alongside human performers, the issues surrounding expressively timed rhythm must be addressed. Current beat tracking methods are not sufficient to follow rhythms automatically when dealing with varying tempo and expressive timing. In the generation of rhythm, some existing interactive systems ignore the pulse entirely, or fix a tempo after some time spent listening to input. Since music unfolds in time, we take the view that musical timing needs to be at the core of a music generation system. Our research explores a connectionist machine learning approach to expressive rhythm generation, based on cognitive and neurological models. Two neural network models are combined within one integrated system. A Gradient Frequency Neural Network (GFNN) models the perception of periodicities by resonating nonlinearly with the musical input, creating a hierarchy of strong and weak oscillations that relate to the metrical structure. A Long Short-term Memory Recurrent Neural Network (LSTM) models longer-term temporal relations based on the GFNN output. The output of the system is a prediction of when in time the next rhythmic event is likely to occur. These predictions can be used to produce new rhythms, forming a generative model. We have trained the system on a dataset of expressively performed piano solos and evaluated its ability to accurately predict rhythmic events. Based on the encouraging results, we conclude that the GFNN-LSTM model has great potential to add the ability to follow and generate expressive rhythmic structures to real-time interactive system

Analytic Controllability of Time-Dependent Quantum Control Systems

The question of controllability is investigated for a quantum control system in which the Hamiltonian operator components carry explicit time dependence which is not under the control of an external agent. We consider the general situation in which the state moves in an infinite-dimensional Hilbert space, a drift term is present, and the operators driving the state evolution may be unbounded. However, considerations are restricted by the assumption that there exists an analytic domain, dense in the state space, on which solutions of the controlled Schrodinger equation may be expressed globally in exponential form. The issue of controllability then naturally focuses on the ability to steer the quantum state on a finite-dimensional submanifold of the unit sphere in Hilbert space -- and thus on analytic controllability. A relatively straightforward strategy allows the extension of Lie-algebraic conditions for strong analytic controllability derived earlier for the simpler, time-independent system in which the drift Hamiltonian and the interaction Hamiltonia have no intrinsic time dependence. Enlarging the state space by one dimension corresponding to the time variable, we construct an augmented control system that can be treated as time-independent. Methods developed by Kunita can then be implemented to establish controllability conditions for the one-dimension-reduced system defined by the original time-dependent Schrodinger control problem. The applicability of the resulting theorem is illustrated with selected examples.Comment: 13 page

NirA is an alternative nitrite reductase from Pseudomonas aeruginosa with potential as an antivirulence target

The opportunistic pathogen Pseudomonas aeruginosa produces an arsenal of virulence factors causing a wide range of diseases in multiple hosts and is difficult to eradicate due to its intrinsic resistance to antibiotics. With the antibacterial pipeline drying up, antivirulence therapy has become an attractive alternative strategy to the traditional use of antibiotics to treat P. aeruginosa infections. To identify P. aeruginosa genes required for virulence in multiple hosts, a random library of Tn5 mutants in strain PAO1-L was previously screened in vitro for those showing pleiotropic effects in the production of virulence phenotypes. Using this strategy, we identified a Tn5 mutant with an insertion in PA4130 showing reduced levels of a number of virulence traits in vitro. Construction of an isogenic mutant in this gene presented results similar to those for the Tn5 mutant. Furthermore, the PA4130 isogenic mutant showed substantial attenuation in disease models of Drosophila melanogaster and Caenorhabditis elegans as well as reduced toxicity in human cell lines. Mice infected with this mutant demonstrated an 80% increased survival rate in acute and agar bead lung infection models. PA4130 codes for a protein with homology to nitrite and sulfite reductases. Overexpression of PA4130 in the presence of the siroheme synthase CysG enabled its purification as a soluble protein. Methyl viologen oxidation assays with purified PA4130 showed that this enzyme is a nitrite reductase operating in a ferredoxin-dependent manner. The preference for nitrite and production of ammonium revealed that PA4130 is an ammonia:ferredoxin nitrite reductase and hence was named NirA. IMPORTANCE The emergence of widespread antimicrobial resistance has led to the need for development of novel therapeutic interventions. Antivirulence strategies are an attractive alternative to classic antimicrobial therapy; however, they require identification of new specific targets which can be exploited in drug discovery programs. The host-specific nature of P. aeruginosa virulence adds complexity to the discovery of these types of targets. Using a sequence of in vitro assays and phylogenetically diverse in vivo disease models, we have identified a PA4130 mutant with reduced production in a number of virulence traits and severe attenuation across all infection models tested. Characterization of PA4130 revealed that it is a ferredoxin-nitrite reductase and hence was named NirA. These results, together with attenuation of nirA mutants in different clinical isolates, high level conservation of its gene product in P. aeruginosa genomes, and the lack of orthologues in human genomes, make NirA an attractive antivirulence target

NirA Is an Alternative Nitrite Reductase from Pseudomonas aeruginosa with Potential as an Antivirulence Target.

The opportunistic pathogen Pseudomonas aeruginosa produces an arsenal of virulence factors causing a wide range of diseases in multiple hosts and is difficult to eradicate due to its intrinsic resistance to antibiotics. With the antibacterial pipeline drying up, antivirulence therapy has become an attractive alternative strategy to the traditional use of antibiotics to treat P. aeruginosa infections. To identify P. aeruginosa genes required for virulence in multiple hosts, a random library of Tn5 mutants in strain PAO1-L was previously screened in vitro for those showing pleiotropic effects in the production of virulence phenotypes. Using this strategy, we identified a Tn5 mutant with an insertion in PA4130 showing reduced levels of a number of virulence traits in vitro Construction of an isogenic mutant in this gene presented results similar to those for the Tn5 mutant. Furthermore, the PA4130 isogenic mutant showed substantial attenuation in disease models of Drosophila melanogaster and Caenorhabditis elegans as well as reduced toxicity in human cell lines. Mice infected with this mutant demonstrated an 80% increased survival rate in acute and agar bead lung infection models. PA4130 codes for a protein with homology to nitrite and sulfite reductases. Overexpression of PA4130 in the presence of the siroheme synthase CysG enabled its purification as a soluble protein. Methyl viologen oxidation assays with purified PA4130 showed that this enzyme is a nitrite reductase operating in a ferredoxin-dependent manner. The preference for nitrite and production of ammonium revealed that PA4130 is an ammonia:ferredoxin nitrite reductase and hence was named NirA.IMPORTANCE The emergence of widespread antimicrobial resistance has led to the need for development of novel therapeutic interventions. Antivirulence strategies are an attractive alternative to classic antimicrobial therapy; however, they require identification of new specific targets which can be exploited in drug discovery programs. The host-specific nature of P. aeruginosa virulence adds complexity to the discovery of these types of targets. Using a sequence of in vitro assays and phylogenetically diverse in vivo disease models, we have identified a PA4130 mutant with reduced production in a number of virulence traits and severe attenuation across all infection models tested. Characterization of PA4130 revealed that it is a ferredoxin-nitrite reductase and hence was named NirA. These results, together with attenuation of nirA mutants in different clinical isolates, high level conservation of its gene product in P. aeruginosa genomes, and the lack of orthologues in human genomes, make NirA an attractive antivirulence target

Some perfect cards shuffles (French title: Quelques m\'elanges parfaits de cartes)

In this paper, we study some cards shuffles which are used by magicians. We focus ourselves on the possibility to hit eventually the initial state after several shuffles. This is a classical problem arising in discrete dynamical systems. The computations are performed through an elementary approach, so the paper is easily accessible. ----- Dans cet article, on \'etudie quelques m\'elanges de cartes bien connus du monde de la magie. On examine en d\'etail l'\'eventualit\'e de reconstituer le jeu de cartes initial apr\`es plusieurs m\'elanges cons\'ecutifs. Il s'agit math\'ematiquement d'un probl\`eme de syst\`emes dynamiques discrets pour lequel on recherche explicitement une p\'eriode. Les calculs \'etant pr\'esent\'es de mani\`ere \'el\'ementaire, l'article se veut accessible \`a un large public.Comment: Comments: 22 pages, 16 figures, in Frenc

Optical ‘dampening’ of the refractive error to axial length ratio:implications for outcome measures in myopia control studies

Purpose: To gauge the extent to which differences in the refractive error axial length relationship predicted by geometrical optics are observed in actual refractive/biometric data.Methods: This study is a retrospective analysis of existing data. Right eye refractive error [RX] and axial length [AXL] data were collected on 343 6-to-7-year-old children [mean 7.18 years (SD 0.35)], 294 12-to-13-year-old children [mean 13.12 years (SD 0.32)] and 123 young adults aged 18-to-25-years [mean 20.56 years (SD 1.91)]. Distance RX was measured with the Shin-Nippon NVision-K 5001 infrared open-field autorefractor. Child participants were cyclopleged prior to data collection (1% Cyclopentolate Hydrochloride). Myopia was defined as a mean spherical equivalent [MSE] ≤-0.50D. Axial length was measured using the Zeiss IOLMaster 500. Optical modelling was based on ray tracing and manipulation of parameters of a Gullstrand reduced model eye.Results: There was a myopic shift in mean MSE with age (6-7 years +0.87 D, 12-13 years -0.06 D and 18-25 years -1.41 D), associated with an increase in mean AXL (6-7 years 22.70 mm, 12-13 years 23.49 mm and 18-25 years 23.98 mm). There was a significant negative correlation between MSE and AXL for all age groups (all p <0.005). RX: AXL ratios for participant data were compared with the ratio generated from Gullstrand model eyes. Both modelled and actual data showed non-linearity and non-constancy, and that as axial length is increased, the relationship between myopia and axial length differs, such that it becomes more negative.Conclusions: Optical theory predicts that there will be a reduction in the RX: AXL ratio with longer eyes. The participant data although adhering to this theory show a reduced effect, with eyes with longer axial lengths having a lower refractive error to axial length ratio than predicted by model eye calculations. We propose that in myopia control intervention studies when comparing efficacy, consideration should be given to the dampening effect seen with a longer eye

NirA Is an Alternative Nitrite Reductase from Pseudomonas aeruginosa with Potential as an Antivirulence Target

The opportunistic pathogen Pseudomonas aeruginosa produces an arsenal of virulence factors causing a wide range of diseases in multiple hosts and is difficult to eradicate due to its intrinsic resistance to antibiotics. With the antibacterial pipeline drying up, antivirulence therapy has become an attractive alternative strategy to the traditional use of antibiotics to treat P. aeruginosa infections. To identify P. aeruginosa genes required for virulence in multiple hosts, a random library of Tn5 mutants in strain PAO1-L was previously screened in vitro for those showing pleiotropic effects in the production of virulence phenotypes. Using this strategy, we identified a Tn5 mutant with an insertion in PA4130 showing reduced levels of a number of virulence traits in vitro. Construction of an isogenic mutant in this gene presented results similar to those for the Tn5 mutant. Furthermore, the PA4130 isogenic mutant showed substantial attenuation in disease models of Drosophila melanogaster and Caenorhabditis elegans as well as reduced toxicity in human cell lines. Mice infected with this mutant demonstrated an 80% increased survival rate in acute and agar bead lung infection models. PA4130 codes for a protein with homology to nitrite and sulfite reductases. Overexpression of PA4130 in the presence of the siroheme synthase CysG enabled its purification as a soluble protein. Methyl viologen oxidation assays with purified PA4130 showed that this enzyme is a nitrite reductase operating in a ferredoxin-dependent manner. The preference for nitrite and production of ammonium revealed that PA4130 is an ammonia:ferredoxin nitrite reductase and hence was named NirA