Gestural communication of music structure during solo classical piano performance

The production and perception of music is a multimodal activity involving auditory, visual and conceptual processing, integrating these with prior knowledge and environmental experience. Musicians utilise expressive physical nuances to highlight salient features of the score. The question arises within the literature as to whether performers’ non-technical, non-sound-producing movements may be communicatively meaningful and convey important structural information to audience members and co-performers. In the light of previous performance research (Vines et al., 2006, Wanderley, 2002, Davidson, 1993), and considering findings within co-speech gestural research and auditory and audio-visual neuroscience, this thesis examines the nature of those movements not directly necessary for the production of sound, and their particular influence on audience perception. Within the current research 3D performance analysis is conducted using the Vicon 12- camera system and Nexus data-processing software. Performance gestures are identified as repeated patterns of motion relating to music structure, which not only express phrasing and structural hierarchy but are consistently and accurately interpreted as such by a perceiving audience. Gestural characteristics are analysed across performers and performance style using two Chopin preludes selected for their diverse yet comparable structures (Opus 28:7 and 6). Effects on perceptual judgements of presentation modes (visual-only, auditory-only, audiovisual, full- and point-light) and viewing conditions are explored. This thesis argues that while performance style is highly idiosyncratic, piano performers reliably generate structural gestures through repeated patterns of upper-body movement. The shapes and locations of phrasing motions are identified particular to the sample of performers investigated. Findings demonstrate that despite the personalised nature of the gestures, performers use increased velocity of movements to emphasise musical structure and that observers accurately and consistently locate phrasing junctures where these patterns and variation in motion magnitude, shape and velocity occur. By viewing performance motions in polar (spherical) rather than cartesian coordinate space it is possible to get mathematically closer to the movement generated by each of the nine performers, revealing distinct patterns of motion relating to phrasing structures, regardless of intended performance style. These patterns are highly individualised both to each performer and performed piece. Instantaneous velocity analysis indicates a right-directed bias of performance motion variation at salient structural features within individual performances. Perceptual analyses demonstrate that audience members are able to accurately and effectively detect phrasing structure from performance motion alone. This ability persists even for degraded point-light performances, where all extraneous environmental information has been removed. The relative contributions of audio, visual and audiovisual judgements demonstrate that the visual component of a performance does positively impact on the over- all accuracy of phrasing judgements, indicating that receivers are most effective in their recognition of structural segmentations when they can both see and hear a performance. Observers appear to make use of a rapid online judgement heuristics, adjusting response processes quickly to adapt and perform accurately across multiple modes of presentation and performance style. In line with existent theories within the literature, it is proposed that this processing ability may be related to cognitive and perceptual interpretation of syntax within gestural communication during social interaction and speech. Findings of this research may have future impact on performance pedagogy, computational analysis and performance research, as well as potentially influencing future investigations of the cognitive aspects of musical and gestural understanding.

The development and field test of a Mealtime Interaction Clinical Observation Tool: a pilot study and clinical research portfolio

Objective: The purpose of this study was to develop and test psychometric properties of a Mealtime Interaction Clinical Observation Tool (MICOT) that could be used to facilitate assessment and behavioural intervention in childhood feeding difficulties. Methods: Thematic analysis of four focus groups with feeding and behaviour experts identified the content and structure of the MICOT. Following refinement, inter-rater reliability was tested between three healthcare professionals. Results: Six themes were identified for the MICOT, which utilises a traffic-light system to identify areas of strength and areas for intervention. Despite poor inter-rater reliability, for which a number of reasons are postulated, some correlation between psychologists’ ratings was evident. Healthcare professionals liked the tool and reported that it could have good clinical utility. Conclusion: The study provides a promising first version of a clinical observation tool that facilitates assessment and behavioural intervention in childhood feeding difficulties.

The bacterial helicase-primase interaction: a common structural/functional module

The lack of a high-resolution structure for the bacterial helicase-primase complex and the fragmented structural information for the individual proteins have been hindering our detailed understanding of this crucial binary protein interaction. Two new structures for the helicase-interacting domain of the bacterial primases from Escherichia coli and Bacillus stearothermophilus have recently been solved and both revealed a unique and surprising structural similarity to the amino-terminal domain of the helicase itself. In this minireview, the current data are discussed and important new structural and functional aspects of the helicase-primase interaction are highlighted. An attractive structural model with direct biological significance for the function of this complex and also for the development of new antibacterial compounds is examined.

Crystal structure of Bn IV in complex with myristic acid: A Lys49 myotoxic phospholipase A(2) from Bothrops neuwiedi venom

The LY549-PLA(2)s myotoxins have attracted attention as models for the induction of myonecrosis by a catalytically independent mechanism of action. Structural studies and biological activities have demonstrated that the myotoxic activity of LYS49-PLA(2) is independent of the catalytic activity site. The myotoxic effect is conventionally thought to be to due to the C-terminal region 111-121, which plays an effective role in membrane damage. In the present study, Bn IV LYS49-PLA(2) was isolated from Bothrops neuwiedi snake venom in complex with myristic acid (CH3(CH2)(12)COOH) and its overall structure was refined at 2.2 angstrom resolution. The Bn IV crystals belong to monoclinic space group P2(1) and contain a dimer in the asymmetric unit. The unit cell parameters are a = 38.8, b = 70.4, c = 44.0 angstrom. The biological assembly is a "conventional dimer" and the results confirm that dimer formation is not relevant to the myotoxic activity. Electron density map analysis of the Bn IV structure shows clearly the presence of myristic acid in catalytic site. The relevant structural features for myotoxic activity are located in the C-terminal region and the Bn IV C-terminal residues NKKYRY are a probable heparin binding domain. These findings indicate that the mechanism of interaction between Bn IV and muscle cell membranes is through some kind of cell signal transduction mediated by heparin complexes. (C) 2010 Elsevier Masson SAS. All rights reserved.

Structural and functional interaction between polyamine related molecules and biological membranes

Changes induced by PA on nucleic acid (NA) conformation and synthesis is proven to be a major reason for PA essentiality (1-3). However, PA interactions with other polyanions, for instance polyanionic membrane lipid bilayers and glyosaminoglycans have received less attention (3-4). The functional importance of these interactions still is an obscure but interesting area of cell and molecular biology, especially in mammalian cells for which specific PA transport systems are not fully characterized (5). In mammals, activity and turnover of the polyamine (PA) synthesis key enzyme is controlled by a set of proteins: Antizymes (OAZ1-3) and antizyme inhibitors (AZIN1 and 2). It is demonstrated that AOZ modulate polyamine uptake (6), and that PA transport to mitochondria is linked to the respiratory chain state and modulates mitochondrial permeability transition (7). Antizyme expression variants have been located in mitochondria, being proposed as a proapoptotic factor (7-8). AZIN 2 is only expressed in a reduced set of tissues that includes mast cells, where it is associated to mast cell granules membrane (9). This fact, together to the abnormalities observed in bone marrow derived mast cell granules when they are differentiated under restricted PA synthesis conditions (10 and unpublished results), point out to important roles of PA and their related proteins in structure and function of mast cell granules. We will also present novel biophysical results on tripartite interactions of PA that remark the interest of the characterization of PA interactions with lipid bilayers for biomedicine and biotechnology. Thus, the information reported in this paper integrates previously reported information with our still unpublished results, all indicating that PA and their related proteins also are important factors for structure and dynamics of biological membranes and their associated functions essential in human physiology; for instance, solute interchange with the environment (uptake and secretion), oxidative metabolism and apoptosis. The importance of these involved processes for human homeostasis claim for further research efforts. 1. Ruiz-Chica J, Medina MA, Sánchez-Jiménez F and Ramírez FJ (2001) Fourier Transform Raman study of the structural specificities on the interaction between DNA and biogenic polyamines. Biophysical J. 80:443-454. 2. Lightfoot HL, Hall J (2014) Endogenous polyamine function--the RNA perspective. Nucleic Acids Res. 42:11275-11290. 3. Igarashi K, Kashiwagi K (2010) Modulation of cellular function by polyamines. Int J Biochem Cell Biol. 42:39-51. 4. Finger S, Schwieger C, Arouri A, Kerth A, Blume A (2014) Interaction of linear polyamines with negatively charged phospholipids: the effect of polyamine charge distance. Biol Chem. 395:769-778. 5. Poulin R, Casero RA, Soulet D. (2012) Recent advances in the molecular biology of metazoan polyamine transport. Amino Acids. 42:711-723. 6. Kahana C (2009) Regulation of cellular polyamine levels and cellular proliferation by antizyme and antizyme inhibitor. Essays Biochem. 4:47-61. 7. Agostinelli E, Marques MP, Calheiros R, Gil FP, Tempera G, Viceconte N, Battaglia V, Grancara S, Toninello A (2010) Polyamines: fundamental characters in chemistry and biology. Amino Acids 38:393-403. 8. Liu GY, Liao YF, Hsu PC, Chang WH, Hsieh MC, Lin CY, Hour TC, Kao MC, Tsay GJ, Hung HC (2006) Antizyme, a natural ornithine decarboxylase inhibitor, induces apoptosis of haematopoietic cells through mitochondrial membrane depolarization and caspases' cascade. Apoptosis 11:1773-1788. 9. Kanerva K, Lappalainen J, Mäkitie LT, Virolainen S, Kovanen PT, Andersson LC (2009). Expression of antizyme inhibitor 2 in mast cells and role of polyamines as selective regulators of serotonin secretion. PLoS One 31:e6858. 10. García-Faroldi G, Rodríguez CE, Urdiales JL, Pérez-Pomares JM, Dávila JC, Pejler G, Sánchez-Jiménez F, Fajardo I (2010) Polyamines are present in mast cell secretory granules and are important for granule homeostasis. PLoS One 30:e15071.

A THEORETICAL STUDY OF INTERACTION OF NANOPARTICLES WITH BIOMOLECULE

Many types of materials at nanoscale are currently being used in everyday life. The production and use of such products based on engineered nanomaterials have raised concerns of the possible risks and hazards associated with these nanomaterials. In order to evaluate and gain a better understanding of their effects on living organisms, we have performed first-principles quantum mechanical calculations and molecular dynamics simulations. Specifically, we will investigate the interaction of nanomaterials including semiconducting quantum dots and metallic nanoparticles with various biological molecules, such as dopamine, DNA nucleobases and lipid membranes. Firstly, interactions of semiconducting CdSe/CdS quantum dots (QDs) with the dopamine and the DNA nucleobase molecules are investigated using similar quantum mechanical approach to the one used for the metallic nanoparticles. A variety of interaction sites are explored. Our results show that small-sized Cd4Se4 and Cd4S4 QDs interact strongly with the DNA nucleobase if a DNA nucleobase has the amide or hydroxyl chemical group. These results indicate that these QDs are suitable for detecting subcellular structures, as also reported by experiments. The next two chapters describe a preparation required for the simulation of nanoparticles interacting with membranes leading to accurate structure models for the membranes. We develop a method for the molecular crystalline structure prediction of 1,2-Dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC), 1,2-Dimyristoyl-sn-glycero-3-phosphorylethanolamine (DMPE) and cyclic di-amino acid peptide using first-principles methods. Since an accurate determination of the structure of an organic crystal is usually an extremely difficult task due to availability of the large number of its conformers, we propose a new computational scheme by applying knowledge of symmetry, structural chemistry and chemical bonding to reduce the sampling size of the conformation space. The interaction of metal nanoparticles with cell membranes is finally carried out by molecular dynamics simulations, and the results are reported in the last chapter. A new force field is developed which accurately describes the interaction forces between the clusters representing small-sized metal nanoparticles and the lipid bilayer molecules. The permeation of nanoparticles into the cell membrane is analyzed together with the RMSD values of the membrane modeled by a lipid bilayer. The simulation results suggest that the AgNPs could cause the same amount of deformation as the AuNPs for the dysfunction of the membrane.

ADVANCED COMPUTATIONAL MODELING OF THE INTERNAL STRUCTURE OF SMART WIND-TURBINE BLADES

Implementation of stable aeroelastic models with the ability to capture the complex features of Multi concept smartblades is a prime step in reducing the uncertainties that come along with blade dynamics. The numerical simulations of fluid structure interaction can thus be used to test a realistic scenarios comprising of full-scale blades at a reasonably low computational cost. A code which was a combination of two advanced numerical models was designed and was run with the help of paralell HPC supercomputer platform. The first model was based on a variation of dimensional reduction technique proposed by Hodges and Yu. This model was the one to record the structural response of heterogenous composite blades. This technique reduces the geometrical complexities of the heterogenous blade section into a stiffness matrix for an equivalent beam. This derived equivalent 1-D strain energy matrix is similar to the actual 3-D strain energy matrix in an asymptotic sense. As this 1-D matrix helps in accurately modeling the blade structure as a 1-D finite element problem, this substantially redues the computational effort and subsequently the computational cost that are required to model the structural dynamics at each step. Second model comprises of implementation of the Blade Element Momentum Theory. In this approach we map all the velocities and the forces with the help of orthogonal matrices that help in capturing the large deformations and the effects of rotations in calculating the aerodynamic forces. This ultimately helps us to take into account the complex flexo torsional deformations. In this thesis we have succesfully tested these computayinal tools developed by MTU’s research team lead by for the aero elastic analysis of wind-turbine blades. The validation in this thesis is majorly based on several experiments done on NREL-5MW blade, as this is widely accepted as a benchmark blade in the wind industry. Along with the use of this innovative model the internal blade structure was also changed to add up to the existing benefits of the already advanced numerical models.

Baran: an interaction-centred user monitoring framework

User Quality of Experience (QoE) is a subjective entity and difficult to measure. One important aspect of it, User Experience (UX), corresponds to the sensory and emotional state of a user. For a user interacting through a User Interface (UI), precise information on how they are using the UI can contribute to understanding their UX, and thereby understanding their QoE. As well as a user’s use of the UI such as clicking, scrolling, touching, or selecting, other real-time digital information about the user such as from smart phone sensors (e.g. accelerometer, light level) and physiological sensors (e.g. heart rate, ECG, EEG) could contribute to understanding UX. Baran is a framework that is designed to capture, record, manage and analyse the User Digital Imprint (UDI) which, is the data structure containing all user context information. Baran simplifies the process of collecting experimental information in Human and Computer Interaction (HCI) studies, by recording comprehensive real-time data for any UI experiment, and making the data available as a standard UDI data structure. This paper presents an overview of the Baran framework, and provides an example of its use to record user interaction and perform some basic analysis of the interaction.

MEF2C: expression, regulation and interaction with target genes in health and diseases

Tese de doutoramento, Ciências Biomédicas, Departamento de Ciências Biomédicas e Medicina, Universidade do Algarve, 2015

Covariant Spectator Theory and Hadron Structure

We present the first results of a study on meson spectroscopy using a covariant formalism based on the Covariant Spectator Theory. Our approach is derived directly in Minkowski space and it approximates the Bethe–Salpeter equation by taking effectively into account the contributions from both ladder and crossed ladder diagrams in the $q\bar{q}$ interaction kernel. A general Lorentz structure of the kernel is tested and chiral constraints on the kernel are discussed. Results for the pion form factor are also presented.

Chiral-symmetry Breaking and Pion Structure in the Covariant Spectator Theory

We introduce a covariant approach in Minkowski space for the description of quarks and mesons that exhibits both chiral-symmetry breaking and confinement. In a simple model for the interquark interaction, the quark mass function is obtained and used in the calculation of the pion form factor. We study the effects of the mass function and the different quark pole contributions on the pion form factor.

New dimeric supramolecular structure of mixed (phthalocyaninato)(porphyrinato)-europium(III) sandwiches : preparation and spectroscopic characteristics

The mixed double-decker Eu\[Pc(15C5)4](TPP) (1) was obtained by base-catalysed tetramerisation of 4,5-dicyanobenzo-15-crown-5 using the half-sandwich complex Eu(TPP)(acac) (acac = acetylacetonate), generated in situ, as the template. For comparative studies, the mixed triple-decker complexes Eu2\[Pc(15C5)4](TPP)2 (2) and Eu2\[Pc(15C5)4]2(TPP) (3) were also synthesised by the raise-by-one-story method. These mixed ring sandwich complexes were characterised by various spectroscopic methods. Up to four one-electron oxidations and two one-electron reductions were revealed by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). As shown by electronic absorption and infrared spectroscopy, supramolecular dimers (SM1 and SM3) were formed from the corresponding double-decker 1 and triple-decker 3 in the presence of potassium ions in MeOH/CHCl3.