Bowing the violin : a case study for auditory-motor pattern modelling in the context of music performance

This project addresses methodological and technological challenges in the development of multi-modal data acquisition and analysis methods for the representation of instrumental playing technique in music performance through auditory-motor patterning models. The case study is violin playing: a multi-modal database of violin performances has been constructed by recording different musicians while playing short exercises on different violins. The exercise set and recording protocol have been designed to sample the space defined by dynamics (from piano to forte) and tone (from sul tasto to sul ponticello), for each bow stroke type being played on each of the four strings (three different pitches per string) at two different tempi. The data, containing audio, video, and motion capture streams, has been processed and segmented to facilitate upcoming analyses. From the acquired motion data, the positions of the instrument string ends and the bow hair ribbon ends are tracked and processed to obtain a number of bowing descriptors suited for a detailed description and analysis of the bow motion patterns taking place during performance. Likewise, a number of sound perceptual attributes are computed from the audio streams. Besides the methodology and the implementation of a number of data acquisition tools, this project introduces preliminary results from analyzing bowing technique on a multi-modal violin performance database that is unique in its class. A further contribution of this project is the data itself, which will be made available to the scientific community through the repovizz platform.

Cytopathology of callus cells infected with grapevine leafroll-associated virus 3

The cytopathology of grapevine (Vitis spp.) callus tissue infected with Grapevine leafroll-associated virus 3 (GLRaV-3), genus Vitivirus was studied in order to investigate the usefulness of callus cultures to study grapevine leafroll-associated viruses. Ultrathin sections were made from in vitro callus obtained from stems and shoots of GLRaV-3 infected grapevine plants. Callus was composed of two types of tissue. Translucent, soft callus was formed and composed of large loosely arranged cells, containing big vacuoles and a thin layer of cytoplasm. Other parts of the callus were brown-coloured and composed of small compactly arranged cells, which showed flexuous and rod-shaped closterovirus-like particles, with 10-12 nm in diameter, at higher magnifications. Groups of vesicles formed by a single membrane were also observed, with sizes ranging from 50-200 nm, containing fine fibrillar material, also typical of closterovirus infections. Virus concentration was monitored by Immunosorbent electron microscopy (ISEM) tests, which showed that in vitro culture of callus tissue from grapevine infected plants, could be used to study the GLRaV viruses through many successive generations, despite the decline in virus concentration after repeated transfers. No virus particles were observed in callus tissue obtained from healthy grapevines.

Novel Players in the Integrin Signaling Orchestra: TCPTP and MDGI

Metastases are the major cause of cancer deaths. Tumor cell dissemination from the primary tumor utilizes dysregulated cellular adhesion and upregulated proteolytic degradation of the extracellular matrix for progeny formation in distant organs. Integrins are transmembrane adhesive receptors mediating cellcell and cellmatrix interactions that are crucial for regulating cell migration, invasion, proliferation, and survival. Consequently, increased integrin activity is associated with augmented migration and invasion capacity in several cancer types. Heterodimeric integrins consist of an alpha - and beta-subunit that are held together in a bent conformation when the receptor is inactive, but extension and separation of subdomains is observed during receptor activation. Either inside-out or outside-in activation of receptors is possible through the intracellular molecule binding to an integrin cytoplasmic domain or extracellular ligand association with an integrin ectodomain, respectively. Several regulatory binding partners have been characterized for integrin cytoplasmic beta-domains, but the regulators interacting with the cytoplasmic alpha-domains have remained elusive. In this study, we performed yeast two-hybrid screens to identify novel binding partners for the cytoplasmic integrin alpha-domains. Further examination of two plausible candidates revealed a significant coregulatory role of an integrin alpha-subunit for cellular signaling processes. T-cell protein tyrosine phosphatase (TCPTP) showed a specific interaction with the cytoplasmic tail of integrin alpha1. This association stimulated TCPTP phosphatase activity, leading to negative regulation of epidermal growth factor receptor (EGFR) signaling and diminished anchorage-independent growth. Another candidate, mammary-derived growth inhibitor (MDGI), exhibited binding to several different integrin cytoplasmic alpha-tails through a conserved GFFKR sequence. MDGI overexpression in breast cancer cells altered EGFR trafficking and caused a remarkable accumulation of EGFR in the cytoplasm. We further demonstrated in vivo that MDGI expression induced a novel form of anti-EGFR therapy resistance. Moreover, MDGI binding to α-tails retained integrin in an inactive conformation attenuating integrin-mediated adhesion, migration, and invasion. In agreement with these results, sustained MDGI expression in breast cancer patients correlated with an increased 10-year distant disease-free survival. Taken together, the integrin signaling network is far from a complete view and future work will doubtless broaden our understanding further.

Competitive ability of corn in coexistence with goosegrass

Competition between plants is one of the main interferences that occurs in agricultural systems and accounts for significant crop yield reductions. The aim of this study was to assess the competitive ability of corn in coexistence with the weed species Eleusine indica. The experiments were conducted in a greenhouse, in the growing season 2010/2011, and were arranged in a completely randomized design with four replications. The experimental units consisted of plastic pots with a volumetric capacity of 8 L. Treatments were arranged in a replacement series with five proportions of corn plants and weed: 100:0, 75:25, 50:50, 25:75, and 0:100, respectively, with a constant population of eight plants per pot, at the end of each treatment. The competitiveness analysis was conducted through diagrams applied to the replacement series experiment and competitiveness index, and the variables evaluated were root, shoot, and total dry mass, and plant height. When in equal proportions, corn showed competitive ability equivalent to goosegrass in relation to the variables shoot, root, and total dry mass. Goosegrass was more competitive than the crop in relation to plant height.

Competitive ability of soybean cultivars with horseweed (Conyza bonariensis)

The existence of large areas infested with populations of Conyza spp. resistant to glyphosate in Brazil demands appropriate and integrated management strategies. This experiment aimed to identify soybean cultivars with greater competitive ability with horseweed plants and to determine plant characteristics associated with this ability. The experiment was arranged in a randomized complete block design with split plots. Seven soybean cultivars (CD 225 RR, BRS 232, CD 226 RR, NK 7054 RR, BMX Apollo RR, BRS 245 RR and BRS 255 RR) were allocated in the plots, and two interference situations (absence and 13.3 plants of Conyza m-2, transplanted seven days before soybean planting) in the subplots. The average yield loss due to competition with horseweed was 25%. Cultivar CD 226 RR showed no significant grain yield loss due to competition, compared to the control without infestation, but showed the lowest average grain yield. The BRS 232 genotype showed loss of grain yield of only 14%, and presented positive plant height and leaf mass at 20 DAE, as well as dry matter of stems+branches in all evaluations, features related to its higher performance and greater ability to withstand competition with horseweed plants.

Adaptive value of ryegrass biotypes with low-level resistance and susceptible to the herbicide fluazifop and competitive ability with the wheat culture

Ryegrass is the main weed in wheat crop, causing yield loss due to competition by environmental resources. The objectives of this study were to estimate the fitness cost of ryegrass biotypes with low-level resistance and susceptible to fluazifop and to investigate the relative competitive ability of these biotypes between themselves and against the crop. Thus, fitness cost and competitive ability experiments were conducted under greenhouse conditions. For the fitness cost experiments, the low-level resistant ryegrass biotypes and those susceptible to fluazifop were used. For competitive ability, the treatments were arranged in a replacement series, with five proportions of the wheat cultivar FUNDACEP Horizonte and the low-level resistant and susceptible ryegrass biotypes 100:0, 75:25, 50:50, 25:75 and 0:100. Competitive analysis was carried out through diagrams applied to the replacement experiments and use of relative competitiveness indices. Variables evaluated were plant height, in the fitness cost experiment, and leaf area and shoot dry biomass in both experiments. The ryegrass biotypes show overall similar fitness cost and competitive ability. The wheat cultivar FUNDACEP Horizonte is superior in competitive ability to the ryegrass biotype with low-level resistance and equivalent to the susceptible biotype.

Does the resistance to glyphosate herbicide affect the competitive ability of ryegrass with soybean?

The objective this work was to investigate the competitive ability between resistant and susceptible ryegrass biotypes and of these with soybean crop. Four experiments were carried under greenhouse, in a completely randomized design with four replications, in 2011 and 2012. Treatments were arranged in additive series and replacement series assay. In each series, the proportions among ryegrass resistant and susceptible plants related to soybean were: 100:0, 75:25, 50:50, 25:75 e 0:100. Leaf area and shoot dry mass were evaluated. Competitiveness statistical analysis consisted in applying diagrams to the replacement series and alternative interpretations of the competitiveness indexes. The soybean crop had equivalent competitiveness to the susceptible ryegrass biotype and inferior to the resistant biotype, while the biotypes, both susceptible and resistant to glyphosate, present equivalent competitive ability. In general, the intraspecific competition is more harmful to ryegrass when in competition with soybean, while interspecific competition is predominant for culture.

Levels of nutrients and grain yield of maize intercropped with signalgrass (Brachiaria) in different arrangements of plants

Competition between maize and signalgrass can economically cripple the intercropping by the reduced yield of maize and dry matter content of the forage. In seeking to define plant arrangements which make this system more efficient, this research was held with the objective of assessing the effects of interference of densities of signalgrass (Urochloa Brizantha) on nutrition and on maize grain yield. Two field experiments were conducted in a randomized block design with four replications. Treatments were arranged similarly in both experiments, in a 2 x 4 factorial design, the first factor being the dose of Nicosulfuron herbicide applied (0 and 8 g ha-1) and the second factor being the forage seeding rates (0, 2, 4 and 6 kg of seeds per hectare). The interference of signalgrass reduced foliar nitrogen, potassium and phosphorus content in maize plants intercropped with the forage. Higher values of grain yield were observed with the reduction of the spacing and the application of the recommended herbicide underdose (8 g ha-1). It was concluded that, regardless of the seeding density of U. Brizantha, reducing the maize seeding inter-rows spacing, combined with the application of an underdose of Nicosulfuron, caused a positive effect by reducing the initial forage growth, resulting in less interference of Urochloa brizantha on nutrient uptake by the maize plants and grain yield of the crop.

COMPETITIVE ABILITY OF CANOLA HYBRIDS WITH WEEDS

ABSTRACTThe objective of the study was to assess the relative competitive ability of canola hybrids in the presence of turnip (Raphanus sativus) and ryegrass (Lolium multiflorum) in different ratios of plants in the mixture. The experiments were conducted in a greenhouse, in a completely randomized design with four replications. Treatments were arranged in ratios of canola against turnip or ryegrass: 100:0, 75:25, 50:50, 25:75 and 0:100. Competitive analysis of the species was accomplished by means of diagrams usually applied to replacement series and also by the relative competitiveness indices. Fifty days after the emergence of the species, measurements of leaf area and shoot dry mass were performed. There was a competition between canola hybrids and weeds, with reduction for all variables. There was a differential competitive ability among canola hybrids in the presence of turnip and/or ryegrass. Canola hybrid Hyola 433 was more competitive in the presence of turnip than Hyola 61, 76 and 571 CL. Hyola 61, 76, 433 and 571 CL do not differ in terms of competition ability when growing with ryegrass.

Glyphosate Herbicide Use in Urochloa brizantha Management in Intercropping With Herbicide-Resistant Maize

The success of the intercropping among cultivated species depends on the adoption of practices that provide, in due course, greater competitive ability of a species over another. The objective of this study was to evaluate the use of glyphosate herbicide in the suppression of Brachiaria (signalgrass) intercropped with maize. The experiment was conducted in a randomized complete block design with four replications. The treatments were arranged in a 5 x 2 + 2 factorial arrangement, the first factor corresponding to the doses of glyphosate (48, 96, 144, 240, 480 g ha-1 of the acid equivalent (a.e)) and the second one to the vegetative stages of the signalgrass at the time of application (2 and 4 tillers). Two controls were added to the treatment list, comprising controls without herbicide application and hand removal of the signalgrass. The number of plants, tillers and dry matter of signalgrass was reduced with glyphosate. The increase of the glyphosate doses enhanced the injure to the forage plants, mainly when the compound was sprayed at the two-tiller vegetative stage. The dry matter of maize plants increased proportionally to the glyphosate dose. However, the height of the maize plants was not affected. The grain mass and productivity of maize grain increased with increasing dose of glyphosate. The maize yield was negatively influenced on the untreated control. Glyphosate at 96 and 144 g ha-1, when applied at 2 and 4 tiller stage, respectively, reduces the growth of signalgrass and does not affect the maize grain yield.

Aircraft tracking and classification with vhf passive bistatic radar

Since the times preceding the Second World War the subject of aircraft tracking has been a core interest to both military and non-military aviation. During subsequent years both technology and configuration of the radars allowed the users to deploy it in numerous fields, such as over-the-horizon radar, ballistic missile early warning systems or forward scatter fences. The latter one was arranged in a bistatic configuration. The bistatic radar has continuously re-emerged over the last eighty years for its intriguing capabilities and challenging configuration and formulation. The bistatic radar arrangement is used as the basis of all the analyzes presented in this work. The aircraft tracking method of VHF Doppler-only information, developed in the first part of this study, is solely based on Doppler frequency readings in relation to time instances of their appearance. The corresponding inverse problem is solved by utilising a multistatic radar scenario with two receivers and one transmitter and using their frequency readings as a base for aircraft trajectory estimation. The quality of the resulting trajectory is then compared with ground-truth information based on ADS-B data. The second part of the study deals with the developement of a method for instantaneous Doppler curve extraction from within a VHF time-frequency representation of the transmitted signal, with a three receivers and one transmitter configuration, based on a priori knowledge of the probability density function of the first order derivative of the Doppler shift, and on a system of blocks for identifying, classifying and predicting the Doppler signal. The extraction capabilities of this set-up are tested with a recorded TV signal and simulated synthetic spectrograms. Further analyzes are devoted to more comprehensive testing of the capabilities of the extraction method. Besides testing the method, the classification of aircraft is performed on the extracted Bistatic Radar Cross Section profiles and the correlation between them for different types of aircraft. In order to properly estimate the profiles, the ADS-B aircraft location information is adjusted based on extracted Doppler frequency and then used for Bistatic Radar Cross Section estimation. The classification is based on seven types of aircraft grouped by their size into three classes.

Promoting Healthy Lifestyles with Personalized, APOE Genotype Based Health Information: The Effects on Psychological-, Health Behavioral and Clinical Factors

There is an increasing demand for individualized, genotype-based health advice. The general population-based dietary recommendations do not always motivate people to change their life-style, and partly following this, cardiovascular diseases (CVD) are a major cause of death in worldwide. Using genotype-based nutrition and health information (e.g. nutrigenetics) in health education is a relatively new approach, although genetic variation is known to cause individual differences in response to dietary factors. Response to changes in dietary fat quality varies, for example, among different APOE genotypes. Research in this field is challenging, because several non-modifiable (genetic, age, sex) and modifiable (e.g. lifestyle, dietary, physical activity) factors together and with interaction affect the risk of life-style related diseases (e.g. CVD). The other challenge is the psychological factors (e.g. anxiety, threat, stress, motivation, attitude), which also have an effect on health behavior. The genotype-based information is always a very sensitive topic, because it can also cause some negative consequences and feelings (e.g. depression, increased anxiety). The aim of this series of studies was firstly to study how individual, genotype-based health information affects an individual’s health form three aspects, and secondly whether this could be one method in the future to prevent lifestyle-related diseases, such as CVD. The first study concentrated on the psychological effects; the focus of the second study was on health behavior effects, and the third study concentrated on clinical effects. In the fourth study of this series, the focus was on all these three aspects and their associations with each other. The genetic risk and health information was the APOE gene and its effects on CVD. To study the effect of APOE genotype-based health information in prevention of CVD, a total of 151 volunteers attended the baseline assessments (T0), of which 122 healthy adults (aged 20 – 67 y) passed the inclusion criteria and started the one-year intervention. The participants (n = 122) were randomized into a control group (n = 61) and an intervention group (n = 61). There were 21 participants in the intervention Ɛ4+ group (including APOE genotypes 3/4 and 4/4) and 40 participants in the intervention Ɛ4- group (including APOE genotypes 2/3 and 3/3). The control group included 61 participants (including APOE genotypes 3/4, 4/4, 2/3, 3/3 and 2/2). The baseline (T0) and follow-up assessments (T1, T2, T3) included detailed measurements of psychological (threat and anxiety experience, stage of change), and behavioral (dietary fat quality, consumption of vegetables, - high fat/sugar foods and –alcohol, physical activity and health and taste attitudes) and clinical factors (total-, LDL- HDL cholesterol, triglycerides, blood pressure, blood glucose (0h and 2h), body mass index, waist circumference and body fat percentage). During the intervention six different communication sessions (lectures on healthy lifestyle and nutrigenomics, health messages by mail, and personal discussion with the doctor) were arranged. The intervention groups (Ɛ4+ and Ɛ4-) received their APOE genotype information and health message at the beginning of the intervention. The control group received their APOE genotype information after the intervention. For the analyses in this dissertation, the results for 106/107 participants were analyzed. In the intervention, there were 16 participants in the high-risk (Ɛ4+) group and 35 in the low-risk (Ɛ4-) group. The control group had 55 participants in studies III-IV and 56 participants in studies I-II. The intervention had both short-term (≤ 6 months) and long-term (12 months) effects on health behavior and clinical factors. The short-term effects were found in dietary fat quality and waist circumference. Dietary fat quality improved more in the Ɛ4+ group than the Ɛ4- and the control groups as the personal, genotype-based health information and waist circumference lowered more in the Ɛ4+ group compared with the control group. Both these changes differed significantly between the Ɛ4+ and control groups (p<0.05). A long-term effect was found in triglyceride values (p<0.05), which lowered more in Ɛ4+ compared with the control group during the intervention. Short-term effects were also found in the threat experience, which increased mostly in the Ɛ4+ group after the genetic feedback (p<0.05), but it decreased after 12 months, although remaining at a higher level compared to the baseline (T0). In addition, Study IV found that changes in the psychological factors (anxiety and threat experience, motivation), health and taste attitudes, and health behaviors (dietary, alcohol consumption, and physical activity) did not directly explain the changes in triglyceride values and waist circumference. However, change caused by a threat experience may have affected the change in triglycerides through total- and HDL cholesterol. In conclusion, this dissertation study has given some indications that individual, genotypebased health information could be one potential option in the future to prevent lifestyle-related diseases in public health care. The results of this study imply that personal genetic information, based on APOE, may have positive effects on dietary fat quality and some cardiovascular risk markers (e.g., improvement in triglyceride values and waist circumference). This study also suggests that psychological factors (e.g. anxiety and threat experience) may not be an obstacle for healthy people to use genotype-based health information to promote healthy lifestyles. However, even in the case of very personal health information, in order to achieve a permanent health behavior change, it is important to include attitudes and other psychological factors (e.g. motivation), as well as intensive repetition and a longer intervention duration. This research will serve as a basis for future studies and its information can be used to develop targeted interventions, including health information based on genotyping that would aim at preventing lifestyle diseases. People’s interest in personalized health advices has increased, while also the costs of genetic screening have decreased. Therefore, generally speaking, it can be assumed that genetic screening as a part of the prevention of lifestyle-related diseases may become more common in the future. In consequence, more research is required about how to make genetic screening a practical tool in public health care, and how to efficiently achieve long-term changes.

3D movement and muscle activity patterns in a violin bowing task

Objective: Overuse injuries in violinists are a problem that has been primarily analyzed through the use of questionnaires. Simultaneous 3D motion analysis and EMG to measure muscle activity has been suggested as a quantitative technique to explore this problem by identifying movement patterns and muscular demands which may predispose violinists to overuse injuries. This multi-disciplinary analysis technique has, so far, had limited use in the music world. The purpose of this study was to use it to characterize the demands of a violin bowing task. Subjects: Twelve injury-free violinists volunteered for the study. The subjects were assigned to a novice or expert group based on playing experience, as determined by questionnaire. Design and Settings: Muscle activity and movement patterns were assessed while violinists played five bowing cycles (one bowing cycle = one down-bow + one up-bow) on each string (G, D, A, E), at a pulse of 4 beats per bow and 100 beats per minute. Measurements: An upper extremity model created using coordinate data from markers placed on the right acromion process, lateral epicondyle of the humerus and ulnar styloid was used to determine minimum and maximum joint angles, ranges of motion (ROM) and angular velocities at the shoulder and elbow of the bowing arm. Muscle activity in right anterior deltoid, biceps brachii and triceps brachii was assessed during maximal voluntary contractions (MVC) and during the playing task. Data were analysed for significant differences across the strings and between experience groups. Results: Elbow flexion/extension ROM was similar across strings for both groups. Shoulder flexion/extension ROM increaslarger for the experts. Angular velocity changes mirrored changes in ROM. Deltoid was the most active of the muscles assessed (20% MVC) and displayed a pattern of constant activation to maintain shoulder abduction. Biceps and triceps were less active (4 - 12% MVC) and showed a more periodic 'on and off pattern. Novices' muscle activity was higher in all cases. Experts' muscle activity showed a consistent pattern across strings, whereas the novices were more irregular. The agonist-antagonist roles of biceps and triceps during the bowing motion were clearly defined in the expert group, but not as apparent in the novice group. Conclusions: Bowing movement appears to be controlled by the shoulder rather than the elbow as shoulder ROM changed across strings while elbow ROM remained the same. Shoulder injuries are probably due to repetition as the muscle activity required for the movement is small. Experts require a smaller amount of muscle activity to perform the movement, possibly due to more efficient muscle activation patterns as a result of practice. This quantitative multidisciplinary approach to analysing violinists' movements can contribute to fuller understanding of both playing demands and injury mechanisms .

Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

De l'ethnicité dans les langages musicaux contemporains : au-delà de l'exotisme : processus de composition de quatre oeuvres : Deux tempêtes et une langueur, Sept gestes ludiques, Azabache, Landocinogena

La version intégrale de ce mémoire est disponible uniquement pour consultation individuelle à la Bibliothèque de musique de l’Université de Montréal.