Dissertations / Theses on the topic 'Locally coherent'

The main goal of this study is to propose a methodology that measures directed relations between locally stationary processes. Unlike stationary processes, locally stationary processes may present sudden pattern changes and have local characteristics in specific intervals. This behavior causes instability in measures based on Fourier transforms. The relevance of this study relies on considering these processes and propose robust methodologies that are not affected by outliers, sudden pattern changes or local behavior. We start reviewing the Partial Directed Coherence (PDC) and the Wavelet Coherence. PDC measures the directed relation between components of a multivariate stationary Vector Autoregressive (VAR) model in the frequency domain, while Wavelet Coherence is based on complex wavelets decomposition. We then propose a causal wavelet decomposition of the covariance structure for bivariate locally stationary processes: the Directed Wavelet Covariance (DWC). Compared to Fourier-based quantities, wavelet-based estimators are more appropriate for non-stationary processes and processes with local patterns, outliers and rapid regime changes like in EEG experiments with the introduction of stimuli. We then propose its estimators and calculate its expectation and analyze its variance. Next we propose a decomposition for the variance of multivariate processes with more than two components: the Partial Directed Wavelet Covariance (pDWC). Considering a N-variate locally stationary process, the pDWC calculates the Directed Wavelet Covariance of X_1(t) with X_2(t) eliminating the effect of the other components X_3(t), ... ,X_N(t). We propose two approaches to this situation. First we filter the multivariate process to remove all the exogenous influences and then we calculate the directed relation between the components. In the second case, as in Partial Directed Coherence, we consider the multivariate process as a time-varying Vector Autoregressive Model (tv-VAR) and use its coefficients in the decomposition of the covariance function to isolate the effects of the other components. We also compare results of the PDC, Wavelet Coherence and Directed Wavelet Covariance with simulated data. Finally, we present an application of the proposed Directed Wavelet Covariance and Partial Directed Wavelet Covariance on EEG data. Simulation results show that the proposed measures capture the simulated relations. The pDWC with linear filter has shown more stable estimations than the proposed pDWC considering the tv-VAR. Future studies will discuss the DWC\'s and pDWC\'s asymptotic distributions and significance tests. The proposed Directed Wavelet Covariance decomposition is a different approach to deal with non-stationary processes in the context of causality. The use of wavelets is a gain and adds to the number of studies that can be addressed when Fourier transform does not apply. The pDWC is an alternative for multivariate processes and it removes linear influences from observed external components.<br>O objetivo deste trabalho é propor uma metodologia para mensurar o impacto direcionado entre processos localmente estacionários. Diferente de processos estacionários, processos localmente estacionários podem apresentar mudanças bruscas e características específicas em determinados intervalos. Tal comportamento pode causar instabilidade em medidas baseadas na transformada de Fourier. A importância deste estudo se dá em englobar processos com tais características, propondo metodologias robustas que não são afetadas pela existência de mudanças bruscas, pontos discrepantes e comportamentos locais. Inicialmente apresentamos conceitos já existentes na literatura, como a Coerência Parcial Direcionada (PDC) e a Coerência de Ondaletas. A PDC mede o impacto direcionado entre componentes de um modelo vetorial autoregressivo (VAR) no domínio da frequência. A coerência de ondaletas é baseada em transformadas complexas de ondaletas. Propomos então uma decomposição no domínio de ondaletas para a estrutura de covariância de processos bivariados localmente estacionários: a Covariância Direcionada de Ondaletas (DWC). Em comparação com as quantidades baseadas na tranformada Fourier, os estimadores baseados em ondaletas são mais apropriados para processos não estacionários com padrões locais, pontos discrepantes ou mudanças rápidas de regime, como em experimentos de eletroencefalograma (EEG) com a introdução de estímulo. Ainda, propomos um estimador para a DWC, calculamos a esperança deste estimador e avaliamos sua variância. Em seguida, propomos uma quantidade análoga à DWC para processos multivariados com mais de duas componentes: a Covariância Parcial Direcionada de Ondaletas (pDWC). Considerando um processo N-variado localmente estacionário, a pDWC calcula a Covariância Direcionada de Ondaletas entre X_1(t) e X_2(t) eliminando o efeito das outras componentes X_3(t), ... , X_N(t). Propomos duas abordagens para a pDWC: na primeira, a pDWC é calculada após a aplicação de um filtro linear que remove o efeito das variáveis exógenas. No segundo caso, a exemplo da Coerência Parcial Direcionada, consideramos o processo multivariado como um Modelo Autoregressivo de Vetorial variante no tempo (tv-VAR) e usamos seus coeficientes na decomposição da função de covariância para isolar os efeitos das demais componentes. Também comparamos os resultados da PDC, Coerência de Ondaletas e Covariância Direcionada de Ondaletas com dados simulados. Por fim, apresentamos uma aplicação da DWC e da pDWC em dados de EEG. Identificamos nas simulações que tanto as medidas já existentes na literatura quanto as quantidades propostas identificaram as relações simuladas. A pDWC proposta com filtros lineares apresentou estimações mais estáveis do que a pDWC considerando os modelos tv-VAR. Estudos futuros discutirão as propriedades assintóticas e testes de significância da DWC e pDWC.

Large scale functional brain networks, defined by synchronized spontaneous oscillations between spatially distinct anatomical regions, are essential to brain function and have been implicated in disease states, cognitive capacity, and many sensing and motor processes. In this work, we sever the corpus callosum in the rodent model to determine if structural connectivity (specifically the primary interhemispheric pathway) organizes and influences bilateral functional connectivity and brain-wide spatiotemporal dynamic activity patterns. Prior to the callosotomy work, resting state brain networks were evaluated using blood oxygen level dependent (BOLD) and cerebral blood volume (CBV) magnetic resonance imaging contrast mechanisms, and revealed that BOLD and CBV provide highly similar spatial maps of functional connectivity; however, the amplitude of BOLD connectivity was generally stronger. The effects of extended anesthetic durations on functional connectivity were also evaluated revealing extended isoflurane anesthetic periods prior to the switch to dexmedetomidine attenuates functional activity for a longer duration as compared to a shorter isoflurane paradigm. We also observed a secondary significant evolution of functional metrics occurring during long durations of dexmedetomidine use under the currently accepted and refined dexmedetomidine sedation paradigm. Taking these previous findings into account, we moved forward with the callosotomy study. Functional network integrity was evaluated in sham and full callosotomy groups using BOLD and electrophysiology. Functional connectivity analysis indicated a similar significant reduction in bilateral connectivity in the full callosotomy group as compared to the sham group across both recording modalities. Spatiotemporal dynamic analysis revealed bilaterally symmetric propagating waves of activity in the sham data, but none were present in the full callosotomy data; however, the emergence of unilateral spatiotemporal patterns became prominent following the callosotomy. This finding suggests that the corpus callosum could be largely responsible for maintaining bilateral network integrity, but non-bilaterally symmetric propagating waves occur in the absence of the corpus callosum, suggesting a possible subcortical driver of the dynamic cascading event. This work represents a robust finding indicating the corpus callosum's influence on maintaining integrity in bilateral functional networks.

L’imagerie échographique a connu un fort développement ces dernières années. Elle possède une cadence d’imagerie allant jusqu’à plusieurs milliers d’images par secondes notamment avec l’émergence des méthodes dites ultrarapides. Il s’agit donc de la modalité la plus adaptée pour des applications cardiaques permettant non seulement la reconstruction d’images mais également l’extraction de paramètres pour la caractérisation tissulaire, comme l’anisotropie locale présente dans le cœur. En effet, cet arrangement fibreux peut être modifié dans le cas de pathologies cardiaques. L’objectif de ce travail de doctorat est le développement d’une méthode d’extraction par imagerie ultrasonore 3D de l’orientation locale d’un milieu anisotrope. Cette approche doit permettre l’imagerie avec un large champ de vue pour être appliquée en imagerie cardiaque. Enfin, la validation de la chaîne de traitement est nécessaire. Pour répondre à ces problématiques, plusieurs solutions ont été proposées. Tout d’abord, l’orientation locale a été évaluée grâce à une méthode de cohérence spatiale permettant l’estimation de l’orientation dans un plan parallèle à la surface de la sonde. Une fois mise au point et validée, cette stratégie a été étendue afin d’extraire l’orientation locale en 3D et non uniquement l’angle dans un plan. Enfin, l’étude de différents types de transmissions a également été effectuée dans le but d’élargir le champ de vue imagé. Toutes ces méthodes originales ont été appliquées et validées sur des données acquises sur fantôme et in vivo. Ainsi, la détermination de l’orientation locale d’un milieu anisotrope a tout d’abord été réalisée sur un fantôme monodirectionnel puis sur le biceps d’un volontaire. Pour cela, un système expérimental constitué de quatre échographes de recherche a été élaboré grâce à la mise en commun d’équipements de CREATIS et du LabTAU, un autre laboratoire Lyonnais, afin d’acquérir des données en 3D. Ces travaux ont ainsi permis l’extension au cas d’une orientation non parallèle à la surface de la sonde d’un milieu anisotrope ainsi qu’une amélioration en termes de taille de champ de vue de la méthode existante. La validation de toute la chaîne de traitement a été réalisée. L’application au tissu cardiaque in vivo s’inscrit dans les directes perspectives des travaux<br>Ultrasound imaging has strongly developed in recent years. It reaches now a frame rates of several thousand images per second, thanks to the emergence of ultrafast imaging. It is therefore the most suitable modality for cardiac applications. Not only does it allow the reconstruction of images, it also enables the extraction of parameters for tissue characterization, such as local anisotropy inside the heart muscle. Indeed, this fibrous layout can be modified in the case of cardiac pathologies. The aim of this doctoral work is the development of a method to extract the local orientation of an anisotropic environment by 3D ultrasound imaging. This approach should allow imaging with a wide field a view to be applied in cardiac imaging. Finally, the validation of the processing chain is necessary. To address these issues, several solutions have been proposed. First, the local orientation was evaluated using a spatial coherence method. It allowed assessing the orientation of fibres in a plane parallel to the surface of the probe. Once developed and validated, this strategy was extended to extract the local orientation in 3D and not only the angle in a plane. Finally, the study of different types of transmissions was also carried out in order to widen the imaged field of view. All these original methods have been applied and validated on phantom and in vivo data: the determination of the local orientation of an anisotropic environment was first performed on a monodirectional phantom and then on the biceps of a volunteer. For this purpose, an experimental system consisting of four research ultrasound scanners was developed thanks to the sharing of equipment from CREATIS and LabTAU, another laboratory in Lyon, in order to acquire 3D data. This work has thus made it possible both to extend an anisotropic environment to the case of an orientation not parallel to the surface of the probe and to improve the size of the field of view of the existing method. The validation of the entire processing chain has been completed. Applying this method to in vivo cardiac tissue is directly part of future studies

xv, 177 p. : ill. (some col.) A print copy of this thesis is available through the UO Libraries. Search the library catalog for the location and call number.<br>When two or more fluorescent chromophores are closely spaced in a macromolecular complex, dipolar coupling leads to delocalization of the excited states, forming excitons. The relative transition frequencies and magnitudes are sensitive to conformation, which can then be studied with optical spectroscopy. Non-invasive fluorescence spectroscopy techniques are useful tools for the study of dilute concentrations of such naturally fluorescent or fluorescently labeled biological systems. This dissertation presents two phase-selective fluorescence spectroscopy techniques for the study of dynamical processes in bio-molecular systems across a wide range of timescales. Polarization-modulated Fourier imaging correlation spectroscopy (PM-FICS) is a novel phase-selective fluorescence spectroscopy for simultaneous study of translational and conformational dynamics. We utilize modulated polarization and intensity gratings with phase-sensitive signal collection to monitor the collective fluctuations of an ensemble of fluorescent molecules. The translational and conformational dynamics can be separated and analyzed separately to generate 2D spectral densities and joint probability distributions. We present results of PM-FICS experiments on DsRed, a fluorescent protein complex. Detailed information on thermally driven dipole-coupled optical switching pathways is found, for which we propose a conformation transition mechanism. 2D phase-modulation electronic coherence spectroscopy is a third-order nonlinear spectroscopy that uses collinear pulse geometry and acousto-optic phase modulation to isolate rephasing and nonrephasing contributions to the collected fluorescence signal. We generate 2D spectra, from which we are able to determine relative dipole orientations, and therefore structural conformation, in addition to detailed coupling information. We present results of experiments on magnesium tetraphenylporphyrin dimers in lipid vesicle bilayers. The 2D spectra show clearly resolved diagonal and off-diagonal features, evidence of exciton behavior. The amplitudes of the distinct spectral features change on a femtosecond timescale, revealing information on time-dependent energy transfer dynamics. This dissertation includes co-authored and previously published material.<br>Committee in charge: Hailin Wang, Chairperson, Physics; Andrew Marcus, Advisor, Chemistry; Stephen Gregory, Member, Physics; Michael Raymer, Member, Physics; Marina Guenza, Outside Member, Chemistry

Title: Locally Integrated Groups – A special education alternativeAuthor: Jennie ArvidssonType of essay: Exam essay, second level (15 credits)Supervisor: Barbro Bruce, Examiner: Lisbeth OhlssonProgram: Special Education Program at Malmö Högskola, SwedenDate: 2012-01-12Present study is an attempt to describe how staff perceive their working operations in seven locally integrated groups, for pupils in special educational needs. By submitting a questionnaire to all professions within the groups I have tried to find similarities and differences in their statements from both structured and unstructured questions. The study is an attempt to contribute knowledge about how these groups can be understood and developed, based on a special education perspective, systems theory and sense of coherence (KASAM). The results shows that there is a consensus among the majority of staff opinions of the systems’ opportunities as well as dilemmas. On the other hand, it is possible to discern some differences in how the different professions describe their working operations according to how satisfied they are with didactic activities, interaction with others and the resources the groups has at its disposal. The basis for these differences lies in a variety of factors that have an effect on the staff opinions.Retrospectively, the study shows that the staff of the local integrated groups are looking for a central control of operations, and a clearer formulation of goals and visions. The staff also expressed a desire to establish a network between the groups, which may contribute to an exchange of experiences and increase the feeling of togetherness. More time for planning, developing further skills and continuous supervision are other resources that are sought after.

Article shows presence of the imbalance caused by insufficient level of productivity of modern and perspective information communication technologies concerning information intensity of bit streams. It is described how imbalance level reducing can be formed as a result of increasing of information processing technologies efficiency and that JPEG platform is the basic concept for construction of technologies of compression representation. Therefore it is proposed to provide further development of video processing methods using individual components of the JPEG platform for improving the integrity of information in terms of ensuring the required level of its availability.:

Thesis (Ed.D.)--Boston University<br>This study focused on 12th grade Chilean students' ability to produce locally coherent academic texts and on the cognitive basis that underlies this ability. Participants were Chilean students from the city of Santiago, who attended urban public schools, belonged to a low socioeconomic group, and had obtained average scores on the national literacy assessment (SIMCE). All the students in the study wrote argumentative texts in response to a writing prompt and answered a test of recognition of incoherent sequences. A sub sample wrote a second argumentative text while thinking aloud and, immediately after, they had a semi structured interview with the researcher in which the relationship between the ideas included in their texts was discussed. Quantitative and qualitative methods were used in order to analyze local coherence in students' written products, and the relation between these products and students' ability to recognize, explain and self-regulate local coherence during writing. Students who recognized most incoherent sequences were more able to explain local coherence relations, tended to self-regulate writing, and produced texts that were mostly coherent and that exhibited an incipient command of the resources associated to coherent academic writing. Students who recognized none or few incoherent sequences had trouble explaining local coherence relations, did not self-regulate writing, and produced texts that were mostly coherent but that exhibited poor command of the resources associated to coherence in academic writing. In addition, the majority of students in the high recognition group recalled some kind of instruction on local coherence, while the majority of students in the low recognition group could not remember receiving such instruction. Findings suggest that having command of the resources typical of oral language coherence suffices for composing mostly coherent texts, although such writing does not resemble the academic structures. Specifically, contents are not transformed by virtue of logical operators that could reflect a more analytical or critical thinking. It is suggested that being able to use local coherence resources typical of academic writing is associated to having specific knowledge and a self regulated behavior during the writing process.

A sumarização multidocumento consiste na tarefa de produzir automaticamente um único sumário a partir de um conjunto de textos derivados de um mesmo assunto. É imprescindível que seja feito o tratamento de fenômenos que ocorrem neste cenário, tais como: (i) a redundância, a complementaridade e a contradição de informações; (ii) a uniformização de estilos de escrita; (iii) tratamento de expressões referenciais; (iv) a manutenção de focos e perspectivas diferentes nos textos; (v) e a ordenação temporal das informações no sumário. O tratamento de tais fenômenos contribui significativamente para que seja produzido ao final um sumário informativo e coerente, características difíceis de serem garantidas ainda que por um humano. Um tipo particular de coerência estudado nesta tese é a coerência local, a qual é definida por meio de relações entre enunciados (unidades menores) em uma sequência de sentenças, de modo a garantir que os relacionamentos contribuirão para a construção do sentido do texto em sua totalidade. Partindo do pressuposto de que o uso de conhecimento discursivo pode melhorar a avaliação da coerência local, o presente trabalho propõe-se a investigar o uso de relações discursivas para elaborar modelos de coerência local, os quais são capazes de distinguir automaticamente sumários coerentes dos incoerentes. Além disso, um estudo sobre os erros que afetam a Qualidade Linguística dos sumários foi realizado com o propósito de verificar quais são os erros que afetam a coerência local dos sumários, se os modelos de coerência podem identificar tais erros e se há alguma relação entre os modelos de coerência e a informatividade dos sumários. Para a realização desta pesquisa foi necessário fazer o uso das informações semântico-discursivas dos modelos CST (Cross-document Structure Theory) e RST (Rhetorical Structure Theory) anotadas no córpus, de ferramentas automáticas, como o parser Palavras e de algoritmos que extraíram informações do córpus. Os resultados mostraram que o uso de informações semântico-discursivas foi bem sucedido na distinção dos sumários coerentes dos incoerentes e que os modelos de coerência implementados nesta tese podem ser usados na identificação de erros da qualidade linguística que afetam a coerência local.<br>Multi-document summarization is the task of automatically producing a single summary from a collection of texts derived from the same subject. It is essential to treat many phenomena, such as: (i) redundancy, complementarity and contradiction of information; (ii) writing styles standardization; (iii) treatment of referential expressions; (iv) text focus and different perspectives; (v) and temporal ordering of information in the summary. The treatment of these phenomena contributes to the informativeness and coherence of the final summary. A particular type of coherence studied in this thesis is the local coherence, which is defined by the relationship between statements (smallest units) in a sequence of sentences. The local coherence contributes to the construction of textual meaning in its totality. Assuming that the use of discursive knowledge can improve the evaluation of the local coherence, this thesis proposes to investigate the use of discursive relations to develop local coherence models, which are able to automatically distinguish coherent summaries from incoherent ones. In addition, a study on the errors that affect the Linguistic Quality of the summaries was conducted in order to verify what are the errors that affect the local coherence of summaries, as well as if the coherence models can identify such errors, and whether there is any relationship between coherence models and informativenessof summaries. For thisresearch, it wasnecessary theuseof semantic-discursive information of CST models (Cross-document Structure Theory) and RST (Rhetorical Structure Theory) annoted in the corpora, automatic tools, parser as Palavras, and algorithms that extract information from the corpus. The results showed that the use of semantic-discursive information was successful on the distinction between coherent and incoherent summaries, and that the information about coherence can be used in error detection of linguistic quality that affect the local coherence.

<p>Ab-initio results of the core-level shift and the distribution about the average for the 3<i>d</i>_5/2 electrons of Ag, Pd and 2<i>p</i>_3/2 of Cu are presented for the face-centered-cubic AgPd and CuPd random alloys. The complete screening model, which includes both initial and final states effects in the same scheme, has been used in the investigations. </p><p>The alloys have been modeled with a supercell containing 256 atoms. Density-functional theory calculations are carried out using the locally self consistent Green's function approach. </p><p>Results from the calculations clearly shows that the core-level shift distributions characteristic is Gaussian, but the components reveals a substantial difference in the FWHM (Full-Width at Half-Maximum). Comparison between the experimental and the calculated broadening shows a remarkable agreement.</p>

2008/2009<br>In this work the turbulent field developing in case of local erosion around a 45° wing-wall bridge abutment was investigated numerically. Three different scour conditions were considered: beginning of the process, logarithmic phase and equilibrium stage. The flow field was computed using a wall-resolving large eddy simulation (a simulation where the near-wall viscous sub-layer is directly resolved) and the bathymetric data were taken from physical experiments with an equivalent geometry. The dynamics of the coherent structures forming around the obstacle and inside the scour-hole was investigated and its influence on the modeling of the problem and on the erosion process was discussed. The analysis suggested that the full dynamics of the vortex system should be directly solved since simple eddy-viscosity models, as the k-ε model in RANS approach, were found to be not suited for this kind of problem and since high-order statistics were found to be important for the evolution of the local scour. The results of the present study may be helpful to formulate new physical-based local scour models to be used for practical evaluation of the scour depth around bridge abutments.<br>XXII Ciclo<br>1981

In reality, dynamic response of a structure supported on a compliant soil may vary significantly from the response of same structure when supported on a rigid base. A parametric study is conducted for the analysis of the variation in the global and the local deformation demands caused by the inertial soil-structure interaction effects. For the purposes of the study, nonlinear dynamic analyses are performed on 7 steel moment-resisting frame models, which are prepared by the virtue of fixed-base and flexible-base (interacting) conditions. Foundation is modeled with the Truncated Cone Model (Wolf, 1994) with the frequency independent coefficients. Free-field earthquake acceleration records are selected to conform to NEHRP equivalent Site Classes C and D. The study is limited to the structures founded on surface rigid mat foundations subjected to vertically propagating horizontally polarized coherent shear waves. Statistical analysis based on multiple linear regression procedure is performed to represent the variation in the response. Within the scope of the study, the wave parameter and the aspect ratio are observed to be directly proportional to the variation in the response, as a general trend. Maximum beneficial contribution of the SSI is found to be 6% in both global and local deformation demands. In addition, the contribution of inertial interaction effects is found to be in a decreasing trend for the increasing levels of ductility demands. Finally, upper limits of wave parameter for H/R=0.5, 1, 2 and 3 are calculated where the variation in the demands are capped at 1.0.

Les problématiques de consommation dans la hiérarchie mémoire sont très présentes dans les architectures actuelles que ce soit pour les systèmes embarqués limités par leurs batteries ou pour les supercalculateurs limités par leurs enveloppes thermiques. Introduire une information de classification dans le système mémoire permet une gestion hétérogène, adaptée à chaque type particulier de données. Nous nous sommes intéressé dans cette thèse plus précisément aux données en lecture seule et étudions les possibilités d’une gestion spécifique dans la hiérarchie mémoire à travers un codesign compilation/architecture. Cela permet d’ouvrir de nouveaux potentiels en terme de localité des données, passage à l’échelle des architectures ou design des mémoires. Evaluée par simulation sur une architecture multi-coeurs, la solution mise en oeuvre permet des gains significatifs en terme de réduction de la consommation d’énergie à performance constante<br>The energy consumption of the memory system in modern architectures is a major issue for embedded system limited by their battery or supercalculators limited by their Thermal Design Power. Using a classification information in the memory system allows a heterogeneous management of data, more specific to each kind of data. During this thesis, we focused on the specific management of read-only data into the memory system through a compilation/architecture codesign. It allows to explore new potentials in terms of data locality, scalability of the system or cache designs. Evaluated by simulation with multi-core architecture, the proposed solution others significant energy consumption reduction while keeping the performance stable

Exploring the concepts of long range aerial transport of microorganisms is the main motivation of this study. For this purpose we use theories and concepts of dynamical systems in the context of geophysical fluid systems. We apply powerful notions such as finite-time Lyapunov exponent (FTLE) and the associated Lagrangian coherent structures (LCS) and we attempt to provide mathematical explanations and frameworks for some applied questions which are based on realistic concerns of atmospheric transport phenomena. Accordingly, we quantify the accuracy of prediction of FTLE-LCS features and we determine the sensitivity of such predictions to forecasting parameters. In addition, we consider the spatiotemporal resolution of the operational data sets and we propose the concept of probabilistic source and destination regions which leads to the definition of stochastic FTLE fields. Moreover, we put forward the idea of using ensemble forecasting to quantify the uncertainty of the forecast results. Finally, we investigate the statistical properties of localized measurements of atmospheric microbial structure and their connections to the concept of local FTLE time-series. Results of this study would pave the way for more efficient models and management strategies for the spread of infectious diseases affecting plants, domestic animals, and humans.<br>Ph. D.

Two codes have been developed and implemented for use on massively parallelsuper computers to simulate two-dimensional and quasi-geostrophic turbulence.The codes have been found to scale well with increasing resolution and width ofthe simulations. This has allowed for the highest resolution simulations of twodimensionaland quasi-geostrophic turbulence so far reported in the literature.The direct numerical simulations have focused on the statistical characteristicsof turbulent cascades of energy and enstrophy, the role of coherent vorticesand departures from universal scaling laws, theoretized more than 40 yearsago. In particular, the investigations have concerned the enstrophy and energycascades in forced and decaying two-dimensional turbulence. Furthermore, theapplicability of Charney’s hypotheses on quasi-geostrophic turbulence has beentested. The results have shed light on the flow evolution at very large Reynoldsnumbers. The most important results are the robustness of the enstrophycascade in forced and decaying two-dimensional turbulence, the sensitivity toan infrared Reynolds number in the spectral scaling of the energy spectrumin the inverse energy cascade range, and the validation of Charney’s predictionson the dynamics of quasi-geostrophic turbulence. It has also been shownthat the scaling of the energy spectrum in the enstrophy cascade is insensitiveto intermittency in higher order statistics, but that corrections apply to the”universal” Batchelor-Kraichnan constant, as a consequence of large-scale dissipationanomalies following a classical remark by Landau (Landau &amp; Lifshitz1987). Another finding is that the inverse energy cascade is maintained bynonlocal triad interactions, which is in contradiction with the classical localityassumption.<br>QC 20101029

Cette thèse s'articule autour de l'étude de la cohérence de la lumière produite à partir de sources de paires de photons intriqués et de micro-lasers. Nous avons produit et manipulé des états photoniques intriqués, et conduit des investigations à la fois fondamentales et appliquées. Les deux études menées sur les aspects fondamentaux de la non localité avaient pour but de relaxer partiellement deux contraintes sur lesquelles s'appuie l'inégalité de Bell standard en vue d'applications à la cryptographie quantique. Ainsi, en collaboration avec l'Université de Genève, nous avons redéfini la notion de localité en prenant en compte les influences sur les mesures de corrélations des choix des configurations expérimentales et d'une efficacité globale de détection limitée. Cela a permis de définir des inégalités de Bell généralisées et les violations expérimentales qui en découlent permettent d'attester de la non localité des états quantiques observés. Nous avons aussi étudié et mis en place une solution expérimentale autorisant l'émission de photons intriqués dans des pairs de canaux télécoms pour la cryptographie quantique. Nous avons montré la préservation de l'intrication sur 150 km et obtenu des débits records en comparaison avec les réalisations similaires. Enfin, nous avons étudié les propriétés de l’émission de lasers à semi-conducteurs aux dimensions réduites. L’émission de ces composants microscopiques s'accompagne de grandes fluctuations en intensité lorsque ceux-ci sont pompés en-dessous du seuil laser. Cette étude a permis de mieux comprendre comment se construit la cohérence laser dans ces systèmes<br>In this thesis we study the coherence of light emitted by entangled photon-pair sources and micro-lasers. We have generated an manipulated entangled photonic states and investigated both fundamental (non locality) and applied (quantum cryptography) research directions. The objective of two fundamental studies on non locality was to partially relax the strong assumptions on which standard Bell tests rely. To this end, we redefined, in collaboration with the University of Geneva, the formalism of locality taking into account the influence, on correlation measurements, of the freedom of choice (in the basis settings) and of the limitation of the overall detection efficiency. Both assumptions allow devising generalized Bell inequalities whose experimental violations indicate that we can still attest for non locality for the observed states. In addition, we have studied and realized an experimental setup allowing to distribute entangled photon pairs in paired telecom channels for high bit rate quantum cryptography. We have shown that entanglement is preserved over a distance of 150 km with record rates for similar realizations, by mimicking classical network solutions exploiting, in an optimal fashion, the capacity of an optical fiber link via dense spectral multiplexing. Finally, we have studied the properties of light emitted by semiconductor lasers showing reduced dimensionality. This micro-lasers actually provide output light under high intensity fluctuations when they are pumped below the threshold. Their study allowed to refine our understanding on how the coherence builds up in these systems as the cavity is filled with photons

Ce mémoire de thèse aborde la caractérisation expérimentale du transfert thermique à l’échelle nanométrique dans des matériaux compatibles avec les procédés de la micro-électronique. Pour cela deux techniques de caractérisation sont appliquées chacune à deux différents systèmes, le silicium mésoporeux irradié et les membranes de silicium suspendues. La première technique de caractérisation est la thermométrie micro-Raman. La puissance du laser chauffe l'échantillon exposé. La détermination de la conductivité thermique nécessite la modélisation de la source de chaleur par la méthode des éléments finis. Dans les cas considérés la modélisation de la source de chaleur repose sur différents paramètres qui doivent être soigneusement déterminés. La seconde technique de caractérisation est la microscopie à sonde locale (d’acronyme anglais SThM), basée sur le principe de la microscopie à force atomique (d’acronyme anglais AFM). Utilisée en mode actif, la sonde AFM est remplacée par une sonde résistive de type Wollaston qui est chauffée par effet Joule. Utilisée en mode AFM contact, cette technique permet une excitation thermique locale du matériau étudié. La détermination de la conductivité thermique nécessite l'analyse de la réponse thermique de la sonde au moyen d'échantillons d'étalonnage et également via la modélisation dans le cas des géométries complexes. L'effet de la position de la pointe sur le transfert de chaleur entre la pointe et l'échantillon est étudié. Une nouvelle méthode de découplage entre le transfert de chaleur entre la pointe et l'échantillon, respectivement à travers l'air et au contact, est proposée pour la détermination de la conductivité thermique des géométries complexes. Les résultats obtenus avec les deux techniques pour les échantillons de silicium mésoporeux irradiés à l’aide d’ions lourds dans le régime électronique sont en bon accord. Ils montrent la dégradation de la conductivité thermique du silicium mésoporeux suite à une augmentation dans la phase d’amorphe lorsque la dose d’irradiation croît. Les résultats obtenus sur les membranes de silicium suspendues montrent une réduction de la conductivité thermique de plus de 50 % par rapport au silicium massif. Lorsque la membrane est perforée périodiquement afin de réaliser une structure phononique de période inférieure à 100 nm, cette réduction est approximativement d’un ordre de grandeur. Un chapitre introduisant un matériau prometteur à base de silicium pour observer des effets de cohérence phononique conclut le manuscrit<br>This PhD thesis deals with the experimental characterization of heat transfer at the nanoscale in materials compatible with microelectronic processes. Two characterization techniques are applied to two different systems, irradiated mesoporous silicon and suspended silicon membranes. The first characterization technique is micro-Raman thermometry. The laser power heats up the exposed sample. The determination of the thermal conductivity requires the modeling of the heat source using finite element simulations. The modeling of the heat source relies on different parameters that should be carefully determined. The second characterization technique is Scanning Thermal Microscopy (SThM), an Atomic Force Microscopy (AFM)-based technique. Operated in its active mode, the AFM probe is replaced by a resistive Wollaston probe that is heated by Joule heating. Used in AFM contact mode, this technique allows a local thermal excitation of the studied material. The determination of the thermal conductivity requires the analysis of the thermal response of the probe using calibration samples and modeling when dealing with complicated geometries. The effect of the tip position on heat transfer between the tip and the sample is studied. A new method decoupling the heat transfer between the tip and the sample, at the contact and through air, is proposed for determining the thermal conductivity of complicated geometries. The results obtained from the two techniques on irradiated mesoporous silicon samples using heavy ions in the electronic regime are in good agreement. They show a degradation of the thermal conductivity of mesoporous silicon due to the increase in the amorphous phase while increasing the ion fluence. The results obtained on suspended silicon membrane strips show a decrease in the thermal conductivity of more than 50 % in comparison to bulk silicon. When perforated into a phononic structure of sub-100 nm period, the membrane thermal conductivity is about one order of magnitude lower than the bulk. A chapter introducing a promising silicon-based material for the evidence of phonon coherence concludes the manuscript

Adopté par l’article 2 de la loi n°2016-1087 de reconquête de la biodiversité, de la nature et des paysages du 8 aout 2016, le principe de solidarité écologique appelle « à prendre en compte, dans toute prise de décision publique ayant une incidence notable sur l’environnement des territoires concernés, les interactions des écosystèmes, des êtres vivants et des milieux naturels ou aménagés ». Ce principe général du droit de l’environnement inscrit à l’article L110-1 du code de l’environnement est destiné à conserver les interactions écosystémiques et les processus écologiques ainsi qu’à améliorer la gestion environnementale des territoires. La dualité de son objet en fait un principe d’une grande richesse, qui devrait concerner de nombreuses décisions. Divers fondements supranationaux, au sein de la jurisprudence et dans les textes internationaux et européens peuvent ainsi lui être attribués. Dans un contexte d’interdépendance écologique, l’évolution de la dimension internationale et européenne du principe reste essentielle pour juger de ses effets au regard de la conservation de la biodiversité. Au niveau du droit interne, son ancrage au cœur de l’équilibre de l’environnement lui apporte un rayonnement particulier. Il conforte le droit à un environnement équilibré et prolonge les principes constitutionnels de prévention et de développement durable. Face à la crise d’extinction mondiale de la biodiversité menaçant notre survie, le principe de solidarité écologique se présente comme cette ultime chance de la conserver. Deux grands ensembles de dispositifs permettent de mesurer la dynamique du principe de solidarité écologique : la trame verte et bleue et la gestion intégrée de la mer et du littoral. Ils constituent une base pour concevoir la solidarité écologique et représentent ainsi le commencement d’un droit nouveau. Le principe de solidarité écologique appelle à les renforcer et, de manière plus générale, à faire évoluer l’ensemble des décisions concernées par le principe<br>Adopted by article 2 from act nr 2016-1087 concerning the reconquest of biodiversity, nature and landscape of August 8th 2016, the principle of ecological solidarity calls “for taking into consideration the interactions of ecosystems, living creatures and natural or developed environments in all public decisions having a notable impact on the environment of the territories concerned”.This general principle of environmental law inscribed in article L110 1 of the environmental code is designed to preserve the interactions of ecosystems and ecological processes as well as to improve the environmental management of the territories. The duality of its objective renders it a highly valuable principle which should be applied to numerous decisions. Various supranational foundations, within jurisprudence and in international and European laws, can thus be assigned to it. In the context of ecological interdependence the evolution of the international and European dimension of the principle remains essential in order to see the benefits concerning the safeguarding of biodiversity. It is greatly enhanced, as regards internal law, by the fact that it is at the very center of the environment's equilibrium. It justifies the right to a balanced environment and extends the constitutional principles of prevention and sustainable development. Confronted with the crisis of world-wide biodiversity extinction that threatens our survival, the principle of ecological solidarity emerges as the last chance to preserve it. Two major groups of systems allow us to measure the dynamics of the principle of ecological solidarity: the green and the blue line belt network and the Ocean and coastline Governance Framework. They constitute a basis on which to develop ecological solidarity and represent the beginnings of new legislation. The principle of ecological solidarity requires them to be reinforced and more generally to advance all decisions concerned by the principle

While task-based functional magnetic resonance imaging (fMRI) has helped us understand the functional role of many regions in the human brain, many diseases and complex behaviors defy explanation. Alternatively, if no task is performed, the fMRI signal between distant, anatomically connected, brain regions is similar over time. These correlations in “resting state” fMRI have been strongly linked to behavior and disease. Previous work primarily calculated correlation in entire fMRI runs of six minutes or more, making understanding the neural underpinnings of these fluctuations difficult. Recently, coordinated dynamic activity on shorter time scales has been observed in resting state fMRI: correlation calculated in comparatively short sliding windows and quasi-periodic (periodic but not constantly active) spatiotemporal patterns. However, little relevance to behavior or underlying neural activity has been demonstrated. This dissertation addresses this problem, first by using 12.3 second windows to demonstrate a behavior-fMRI relationship previously only observed in entire fMRI runs. Second, simultaneous recording of fMRI and electrical signals from the brains of anesthetized rats is used to demonstrate that both types of dynamic activity have strong correlates in electrophysiology. Very slow neural signals correspond to the quasi-periodic patterns, supporting the idea that low-frequency activity organizes large scale information transfer in the brain. This work both validates the use of dynamic analysis of resting state fMRI, and provides a starting point for the investigation of the systemic basis of many neuropsychiatric diseases.

One of the goals of perception is to learn to respond to coherence across space, time and modality. Here we present an abstract framework for the local online unsupervised learning of this coherent information using multi-stream neural networks. The processing units distinguish between feedforward inputs projected from the environment and the lateral, contextual inputs projected from the processing units of other streams. The contextual inputs are used to guide learning towards coherent cross-stream structure. The goal of all the learning algorithms described is to maximize the predictability between each unit output and its context. Many local cost functions may be applied: e.g. mutual information, relative entropy, squared error and covariance. Theoretical and simulation results indicate that, of these, the covariance rule (1) is the only rule that specifically links and learns only those streams with coherent information, (2) can be robustly approximated by a Hebbian rule, (3) is stable with input noise, no pairwise input correlations, and in the discovery of locally less informative components that are coherent globally. In accordance with the parallel nature of the biological substrate, we also show that all the rules scale up with the number of streams.

The rapid increase in demand for bandwidth in optical networks over the last two decades has led to the development of wavelength division multiplexing where multiple channels are transmitted simultaneously at different wavelengths over a single optical-fiber to maximize the usage of the bandwidth available in fiber. Increasing demand for bandwidth has led to narrower channel spacing and the use of advanced modulation schemes that are more spectrally efficient than traditional on-off keying techniques [1]. Nonlinearities and dispersion effects in fiber accumulate over a long distance and can adversely affect the quality of a channel. Hence the ability to measure detailed features of the optical spectrum is crucial to study the performance of a communication link. A conventional optical spectrum analyzer (OSA) based on a diffraction grating has a wide wavelength or frequency scanning range, but suffers from poor frequency resolution. The narrowest resolution bandwidth reported for a grating based OSA is - 0.06nm or 7.5GHz at 1550nm [1]. Various spectral features of interest, such as the transmission spectrum of a laser and modulation spectrum of a channel require sub-picometer resolution, which cannot be achieved by conventional methods using a diffraction grating. High resolution spectrum analyzers (HRSAs) have been built based on heterodyne detection where a portion of the optical spectrum is converted to radio-frequency (RF) with DC corresponding to the local-oscillator (LO) central frequency [3-6]. This is a common technique used in RF-spectrum analyzers. The resolution bandwidth is determined by the electrical bandwidth of the optical receiver. The lowest resolution bandwidth reported is of the order of tens of MHz [6]. Widespread implementation of these instruments however, has been limited owing to their cost and size, one of the major factors being the external cavity (ECT) lasers used as the local-oscillator source in such instruments. We have built a coherent-channel analyzer (CCA) based on balanced coherent detection using a commercial distributed-feedback (DFB) laser as the LO. The use of a DFB laser for the CCA has the potential of reducing the cost of the instrument by at least one-tenth of the price of an HRSA. In this thesis we describe the working of the CCA. We provide an end-to-end system model, analyze the resolution and sensitivity performance of the system, and demonstrate a frequency resolution of 100MHz over the DFB tuning range of 200GHz with a sensitivity of -95dBm. The CCA provides a practical, cost and size effective alternative to the HRSA at the cost of tunability.<br>Graduate

Hiding memory latency is critical in modern machines. Typically, machines have used cache and addressed the ensuing cache coherence problem with hardware or VM-based strategies that rely on global inter-cache communication. However, global communication limits scalability. "Local knowledge" coherence strategies, which use compile-time information to avoid run-time global communication, offer better scalability, but suffer additional cache misses. We develop a framework for understanding the relation of coherence strategies, previous and newly proposed. Within this framework, it is possible to define, independent of implementation considerations, an "ideal" local strategy with respect to cache hit rate. No local strategy could ever do better. For Fortran programs with readily analyzable subscripts, ideal local strategies achieve the same hit rates as global strategies. We develop three new local coherence strategies, CTV, TS1, and TS$\sp\prime$, designed to exploit minimal, aggressive, and reasonable hardware support, respectively. CTV is suitable for machines with no hardware assistance for cache coherence except the bare minimum of an exposed invalidate instruction. TS1 implements the abstract theorems of ideal local coherence as a concrete algorithm. Though the implementation is probably too expensive for a real implementation, TS1 is a vehicle for studying the limits of local coherence. TS$\sp\prime$ treats coherence over array sections as a graph coloring problem. So long as there are sufficient colors (realized as bits per cache line), TS$\sp\prime$ is an ideal local strategy. We found that four colors are adequate for many programs. When more colors are needed, TS$\sp\prime$ degrades gracefully. Its execution overheads are negligible and its hardware implementation costs moderate. Our data shows that TS$\sp\prime$ has better hit rates than the best previous local strategy, time-stamping, for nearly all programs, and thus better expected performance. Our data also shows that TS$\sp\prime$ achieves hit rates equal to global strategies for analyzable programs, and nearly so for partially analyzable programs. We indirectly compared the performance of TS$\sp\prime$ and a particular VM-style global strategy. TS$\sp\prime$ has better expected performance on our test suite. For machines without global coherence hardware, local strategies are an effective approach for an important class of programs.

The ability of humans to perceive significant pattern and structure of an image is something which humans take for granted. We can recognize objects and patterns independent of changes in image contrast and illumination. In the past decades, it has been widely recognized in both biology and computer vision that phase contains critical information in characterizing the structures in images. Despite the importance of local phase information and its significant success in many computer vision and image processing applications, the coherence behavior of local phases at scale-space is not well understood. This thesis concentrates on developing an invariant image representation method based on local phase information. In particular, considerable effort is devoted to study the coherence relationship between local phases at different scales in the vicinity of image features and to develop robust methods to measure the strength of this relationship. A computational framework that computes local phase coherence (LPC) intensity with arbitrary selections in the number of coefficients, scales, as well as the scale ratios between them has been developed. Particularly, we formulate local phase prediction as an optimization problem, where the objective function computes the closeness between true local phase and the predicted phase by LPC. The proposed framework not only facilitates flexible and reliable computation of LPC, but also broadens the potentials of LPC in many applications. We demonstrate the potentials of LPC in a number of image processing applications. Firstly, we have developed a novel sharpness assessment algorithm, identified as LPC-Sharpness Index (LPC-SI), without referencing the original image. LPC-SI is tested using four subject-rated publicly-available image databases, which demonstrates competitive performance when compared with state-of-the-art algorithms. Secondly, a new fusion quality assessment algorithm has been developed to objectively assess the performance of existing fusion algorithms. Validations over our subject-rated multi-exposure multi-focus image database show good correlations between subjective ranking score and the proposed image fusion quality index. Thirdly, the invariant properties of LPC measure have been employed to solve image registration problem where inconsistency in intensity or contrast patterns are the major challenges. LPC map has been utilized to estimate image plane transformation by maximizing weighted mutual information objective function over a range of possible transformations. Finally, the disruption of phase coherence due to blurring process is employed in a multi-focus image fusion algorithm. The algorithm utilizes two activity measures, LPC as sharpness activity measure along with local energy as contrast activity measure. We show that combining these two activity measures result in notable performance improvement in achieving both maximal contrast and maximal sharpness simultaneously at each spatial location.

Modern unsteady (multi-)field visualizations require an effective reduction of the data to be displayed. From a huge amount of information the most informative parts have to be extracted. Instead of the fuzzy application dependent notion of feature, a new approach based on information theoretic concepts is introduced in this paper to detect important regions. This is accomplished by extending the concept of local statistical complexity from finite state cellular automata to discretized (multi-)fields. Thus, informative parts of the data can be highlighted in an application-independent, purely mathematical sense. The new measure can be applied to unsteady multifields on regular grids in any application domain. The ability to detect and visualize important parts is demonstrated using diffusion, flow, and weather simulations.

An ongoing debate is whether people with autism spectrum disorder (ASD) have a local processing bias and to what extent impaired contextual processing is associated with this bias. The set of experiments employed in this project examined global and local processing, shifts between global and local processing, and low- and high-level visual processing in an attempt to address this issue. This thesis tested the hypotheses that (1) a local processing bias is associated with impaired global processing in ASD individuals, and (2) atypical processing style is linked with ASD severity. Twenty ASD individuals and 20 IQ and age (15-30 years) matched normal controls were administered a novel embedded figures task (local processing advantageous), a novel form matching task and novel shape integration task (global processing advantageous), a local-global switching task (which assessed attention broadening and attention narrowing ability), and a local and global motion detection task. The Social Responsiveness Scale was used to assess ASD severity. The ASD group correctly detected significantly more embedded shapes than controls. Compared to controls, ASD participants were disproportionately slower on the shape integration task relative to the form perception task. No overall group differences were found in attention broadening or attention narrowing ability. In addition, no group differences were found in local or global motion perception. Results also revealed a significant correlation between ASD severity and (1) faster response time on the embedded figures test, (2) slower response time on the shape integration task, (3) reduced attention broadening ability, and (4) reduced global motion perception. These findings confirm previous reports of enhanced local visual processing in ASD, and suggest that while global form perception is intact in ASD, global integration is more problematic. There was no evidence of generalized attentional impairments or motion perception abnormalities in ASD participants, suggesting that lower-level perceptual functions may be spared in people with ASD. Perhaps most intriguing was the observed association between ASD severity and enhanced local perception and impaired global processing. This association suggests that both a local processing bias and impaired global processing may play a role in the behavioral aspects of ASD symptomatology.

The dynamical underpinnings of complex computation and information transmission within the brain, while of great interest to the neuroscience community at large, remain poorly understood. One of the striking manifestations of neuronal population activity is that of rhythmic oscillations in the local field potential. It is thought that distinct patterns of these oscillations such as cross-frequency coupling within a given spatial location and coherence between disparate brain regions may represent neuronal computation and communication, respectively. Here we show such dynamics within a human temporal neocortical in vitro model. In specific, we show theta-gamma cross frequency coupling in deep and superficial layers, phase coherence between layers at theta frequencies, and a measure of communication (phase dependent power correlations) between layers at theta frequency. Additionally, we show a novel correlation between communication across layers and cross frequency coupling within layers, demonstrating a dynamic link between local computation and intralaminar communication.

Chui Yuk Lan.<br>Thesis (M.Phil.)--Chinese University of Hong Kong, 1999.<br>Includes bibliographical references (leaves 81-84).<br>Abstracts in English and Chinese.<br>ABSTRACT(ENGLISH AND CHINESE VERSION) --- p.ii<br>ACKNOWLEDGEMENTS --- p.iv<br>TABLE OF CONTENTS --- p.v<br>LIST OF TABLES --- p.viii<br>LIST OF FIGURES --- p.xi<br>LIST OF APPENDICES --- p.xiii<br>Chapter CHAPTER I - --- INTRODUCTION --- p.1<br>Weak Central Coherence Theory --- p.1<br>Superior Spatial Hypothesis --- p.4<br>Superior Segmentation Hypothesis --- p.4<br>Global Precedence Hypothesis --- p.5<br>Perceptual Span Hypothesis --- p.5<br>Main Study-Global and Local Processing Study --- p.6<br>Eye Movement Study --- p.10<br>Purposes of the Present Study --- p.11<br>Chapter CHAPTER II - --- GLOBAL-LOCAL PROCESSING STUDY: METHOD --- p.12<br>Participants --- p.12<br>Apparatus and Setting --- p.12<br>Stimuli --- p.13<br>Design and Procedure --- p.14<br>Chapter CHAPTER III - --- GLOBAL-LOCAL PROCESSING STUDY: RESULTS --- p.19<br>Age and IQ --- p.19<br>Speed-Accuracy Trade Off --- p.19<br>Performance Indices --- p.19<br>Analyses Testing Global Precedence Hypothesis --- p.21<br>Analyses Testing Group Difference on Global/Local Precedence --- p.21<br>Analyses Testing Group Difference on Global-To-Local Interference --- p.24<br>Analyses Testing Group Difference on Local-To-Global Interference --- p.25<br>Analyses Testing the Perceptual Span Hypothesis --- p.39<br>Chapter CHAPTER IV - --- GLOBAL-LOCAL PROCESSING STUDY: DISCUSSION --- p.45<br>Implications of Incompatible Findings with Pervious Studies --- p.45<br>Implications of Partial Support of Global Precedence Hypothesis --- p.47<br>Interpretation of Perceptual Span Hypothesis --- p.50<br>Chapter CHAPTER V - --- EYE-MOVEMENT STUDY: METHOD --- p.51<br>Participants --- p.51<br>Materials --- p.51<br>Apparatus --- p.56<br>Design and Procedure --- p.56<br>Chapter CHAPTER VI - --- EYE-MOVEMENT STUDY: RESULTS --- p.62<br>Age and IQ --- p.62<br>Number of Objects Found in Object Search Tasks --- p.62<br>Total Number of Fixations --- p.62<br>Fixation Duration --- p.62<br>Distance of Fixations --- p.66<br>Fixations Located Outside the Screen --- p.66<br>Fixations Located Within the Screen but Outside the Designated Areas --- p.66<br>Number of Fixations Located Inside the Designated Areas --- p.67<br>Chapter CHAPTER VII - --- EYE-MOVEMENT STUDY: DISCUSSION --- p.73<br>Implications of Eye-Movement Patterns --- p.73<br>Possible Explanations for Eye-Movement Patterns --- p.74<br>Speculation of Faster Information Processing --- p.74<br>Chapter CHAPTER VIII - --- GENERAL DISCUSSION --- p.76<br>Possible Explanations of Global-Local Processing Findings --- p.76<br>Relations to the Weak Central Coherence Theory --- p.77<br>Limitations and Suggestions --- p.79<br>REFERENCES --- p.81<br>APPENDICES --- p.85

This thesis titled, “Nature of Local Interactions at cisPro-Aro Peptide Sequences in Proteins: Evidences for van der Waals type Interactions. Design and Synthesis of Novel Covalent Surrogates for the Peptide Hydrogen Bond”, describes two important studies. The first is to gain a thorough understanding of the nature of interactions that govern cisPro stability at Pro-Aro sequences, which described in the first four chapters. The final chapter describes the synthesis of novel 4-carbon covalent surrogates for the peptide H-bonding interaction. Chapter 1: Local Interactions Governing cisPro Stability: Refining the Model Peptides Chapter 1 Section A: Understanding the role of inter-side chain CH•••Aro interaction in cis-trans isomerization at Pro-Aro and Aro-Pro Sequences. This chapter is divided into two sections. In the first section an exhaustive overview of earlier investigations into the nature of local interactions at Xaa-cisPro-Aro and Aro-cisPro-Xaa peptide sequences, by various groups, are discussed. Most studies have found evidence for the close assemblage between side chains of residues flanking cisPro motifs, when at least one of them is an aromatic group. An electronic C-H•••π nature has been proposed for these assemblies and they are proposed to influence the cisPro stability. We highlight those features in these studies that indicate that these interactions are not always electronically tunable, are insensitive to presence of strong chaotropes in the solvent and occur at protein sequences lacking Pro or cisPro; all of which contradict the electronic C-H•••π model for these inter-side chain assemblages and their perceived influence on cisPro stability. Chapter 1 Section B: Investigation of the Nature of H Xaa•••Aro interaction at Xaa-Pro-Pro-Phe-sequences In Section B, we design and synthesize Pro-Aro containing short peptide models to investigate the nature of local C-H•••Aro interactions in them. We synthesize a series of homologous Pro-Pro-Aro containing peptides (modeled based on earlier studies) and investigate the relative populations of its four Xaa-Pro rotamers using extensive 1D and 2D NMR techniques including TOCSY, HSQC and ROESY. We find several drawbacks that make this a relatively deficient model. Firstly, their relative populations of the rotamers (the most important data for current investigation) cannot be determined with high fidelity as they are dependent on the solvent polarity, solute concentration and chemical shift degeneracy of crucial NMR signals for the rotamers. Importantly, the populations of a few rotamers are influenced by strong 13-membered ring backbone H-bonds. Notably, some of the cisPro rotamers do not even contain the inter-side chain assembly, whose nature is under investigation. Design of novel models – unconstrained by H-bonds We design the Acyl-Pro-Pro-Aro-OMe peptides that lack the possibility of forming the 13-membered ring H-bonded structures. Thorough 1D and 2D NMR analyses of these models reveal that strong Type VI β-turn type 10-membered ring H-bonds are formed in the rotamers of these models – hence precluding their applications for current study. Interestingly, the relative rotamer populations are strongly influenced by solvent polarity and are entirely different from those of the corresponding C-terminal amide models. We further discover that the Pro-Pro-Aro motif is not essential to express the inter-side chain interactions – Ala-Pro-Aro are sufficient. Formation of the 10-membered H-bonding interactions, however, are not precluded. Chapter 2: Design and Synthesis of Acyl-Pro-Phe-OMe: Novel models to investigate the role of HαXaa•••Aro interactions on Xaa-cisPro-Aro stability. Chapter 2 Section A: Design, Synthesis and Conformational Analysis of Ibu-Pro-Phe-OMe Chapter 2 is divided into two sections. In Section A, we replace the amino acid at the N-terminal of the putative Pro residue with simple isosteric isobutyryl group, the resulting minimalist dipeptide model shows the exclusive influence of desired inter-side chain interactions in the cisPro rotamer. Solvent polarity and temperature coefficient studies reveal that absence of any intramolecular H-bonding or Oπ* interactions in it. 1D and 2D NMR analyses clearly indicate the close proximity between the side chains of Ibu and Phe exclusively in the cisPro rotamer. The Kc/t value decreases upon mutation of Phe to Ala. All these features favor the Ibu-Pro-Phe-OMe as an ideal minimalistic model for investigating the nature of Ibu•••Ph assemblages in the cisPro rotamer. Chapter 2 Section B: Investigation of CH•••Aro /Alp•••Alp interactions in Ibu-cisPro-Xaa-OMe In Section B, the 1D and 2D NMR analyses of the complete set of the aliphatic and aromatic analogues Ibu-Pro-Xaa-OMe were investigated. DMSO-d6 was found to be the best solvent for mimicking both the folded and the unfolded local environments of these short peptide sequences. The HαIbu•••Aro assemblage is observed in Aro analogues, but cannot be electronically tuned. The aliphatic analogues also surprisingly contain the HαIbu•••Alp interactions! The Kc/t values (cisPro %) increase in the aliphatic analogues too, where the aliphatic side chain is long. Increase in cisPro stability is not due to ring current effects or intramolecular H-bonds or Oπ* interactions. It seems to be due to van der Waals type interactions between the involved side chains, either of which need not be aromatic in nature. Chapter 3: Nature of Inter-Side Chain Interactions at Acyl-cisPro-Aro Sequences: Evidence for van der Waals Interactions Chapter 3 Section A: Investigation of nature of inter-side chain interactions in R-CO-cisPro-Phe-OMe Chapter 3 has two sections. Section A describes the systematic design and synthesis of Acyl-Pro-Phe-OMe homologues where first the steric bulk and hence the surface area of the aliphatic side chain of the acyl group is varied. Interaction of the phenyl ring of Phe seems to occur with the Cα-Cβ σ-bond of the acyl group. Branching at either Cα or Cβ seems to destabilize the cisPro rotamer. Aliphatic•••Aromatic interactions overwhelm the cisPro rotamer population to be greater than that of transPro. In the analogues where the acidity of the acyl Cα-H bond is increased, the Kc/t does not increase correspondingly. The Δδ(trans-cis) ppm shifts of HαAcyl protons are dependent exclusively on its acidity rather than on the Kc/t values. In carbamyl-Pro, which entirely lack the HαAcyl proton, the Kc/t values are significantly high and improve as the aliphatic surface on the alkoxy group increases. Introduction of benzyloxy carbamyl group at Pro renders almost the same Kc/t values as that of ethyloxy carbamate. All these data contradict the C-H•••π interaction model and strongly support a van der Waals type interaction between the Acyl (preceding cisPro) group’s Xα-Yβ σ-bond and the Aro or Alp side chains (succeeding cisPro). Chapter 3 Section B: Evidence for the Van der Waals nature of Inter Side Chain (Acyl•••S.C.Aro/Alp) interactions- Determination of Interactions energies In Section B, a thorough investigation of both aliphatic•••aliphatic and aliphatic•••aromatic interactions on the background of homologous Acyl-Pro-Aro/Alp-OMe peptide models is undertaken. These models uniquely allow the delineation of contribution of the van der Waals interactions and the ring current effects to the cis/trans isomerization in these peptides. We see that the energy of the van der Waals component of these aliphatic•••aliphatic and aliphatic…aromatic interactions increase linearly with increase in Kc/t, in both DMSO-d6 and D2O. On other hand, energy from the ring current effects largely remains invariant. The Acyl•••Aro/Alp interactions are not hydrophobic and are facilitated by conformational effects. Chapter 4: Crystallographic evidence for van der Waals interaction-mediated stabilization of cisPro conformers Chapter 4 Section A: Systematic crystallization and crystal structure analyses of homologous Xaa-cisPro-Alp and Xaa-cisPro-Aro rotamers: Evidence for van der Waals interactions Chapter 4 has two sections, both of which present crystallographic evidence for the van der Waals nature of the Xaa•••Aro interactions at Xaa-cisPro-Aro sequences. Section A describes the unique crystal structures of five of the Acyl-Pro-Alp-OMe analogues that have been synthesized in the current study. All of them remarkably crystallize with two features: 1) the Acyl-Pro peptide bond adopts the cisPro rotamer in all; and 2) the aliphatic side chains of the acyl group and the Alp side chain are involved in van der Waals type interactions. The cisPro rotamers of even the bulkiest motifs, namely Ibu-Pro-Val-OMe, Piv-Pro-Ile-OMe and Piv-Pro-Leu-OMe crystallize, stabilized by van der Waals packing between aliphatic groups of the acyl and the Leu/Ile/Val side chains. Where the side chains are not long enough to make sub-van der Waals contacts with each other, their acyl C′-Cα σ-bond rotations are restricted due to Oσ* interactions involving the charge on the acyl carbonyl O. Where this occurs, the short space between the acyl and Alp side chains are filled in by aliphatic groups from neighbouring molecules at sub van der Waals distances. The Pro, Alp and χ1(Alp) dihedral angles are restricted to narrow range of values, irrespective of the length of Alp side chain, indicating that this backbone conformation is a conformational minimum when i+3i backbone H-bond is removed, with Pro at the i+1st position. This is further substantiated in Piv-Pro-Gly-OMe, which crystallizes in trans-Pro form, but still adopts similar backbone dihedral angles in spite of lacking any Alp side chain for interactions with the acyl group. Three of the Acyl-Pro-Aro-OMe models also crystallize in cisPro rotamer forms – both exhibit van der Waals type contacts between the Acyl group and backbone of Phe, rather than the aromatic ring of Phe. The phenyl ring of Phe may or may not form intramolecular Ph•••Pro inter-side chain contacts – which is not a pre-requisite for cisPro stabilization. No C-H••• interactions are observed anywhere in these peptides – van der Waals type contacts alone predominate in all cases. There are no abnormal distortions in bond angles or lengths even in the most sterically hindered cases, signifying that the conformations of these cisPro rotamers involving aliphatic•••aliphatic type contacts are natural minima. Chapter 4 Section B: Mining the PDB for Statistical Evidence of van der Waals interactions Section B of chapter 4 describes the data mining and statistical analyses of Xaa-cisPro-Phe, Xaa-cisPro-Val and Xaa-cisProLeu sequences in the PDB. The PEARL program was used to mine the PDB data. The overall frequency of 5.3% for appearance of cisPro among all Xaa-Pro peptide bonds, improves when Xaa is Phe or Tyr. However, several anomalies highlight the need for refining the analyses set to only those sequences where the side chains of Xaa and Aro/Alp face each other. In this refined set, clearly, inter side chain Xaa•••Alp/Aro contacts take precedence over even Aro•••Pro interactions at Aro-cisPro sequences (where Xaa is Aro). The Phe and the Leu side chains induce similar conformational effects on the preceding Xaa-Pro backbone. So does Val. Strong aliphatic•••aliphatic inter side chain contacts at van der Waals distances are observed to flank cisPro in several proteins. Substitution at the Cα of Xaa governs the proximity of the approaching side chain of Alp / Aro residue. The Cα-H of Xaa steers away from the Aro side chain at Xaa-Pro-Phe sequences, as the Aro group gets closer to it – implying the absence of ordered C-H••• contacts between them. There is consistent parallel alignment between Cα-Cβ -bond of Xaa and the C -C bond of the approaching side chain of Alp or Aro group – clearly highlighting the presence of van der Waals type interactions between them. All these evidences clearly point towards the van der Waals nature of local interactions at cisPro-Aro/Alp peptide sequences. Chapter 5: A novel 4-carbon covalent surrogate model for peptide H-Bond Chapter 5 describes the design and synthesis of novel 4-carbon covalent surrogates for the peptide H-bond (HBS). These surrogates would allow the unique constraining of two peptide strands in their extended conformations. The covalent HBS contain four orthogonal functional groups for independent extension at all of the four ends – similar to an endogenous inter-strand peptide H-bond. The synthesis of the surrogate is achieved by directly using natural chiral amino acid derivatives, beginning from amino alcohols obtained from reduction of desired amino acids. Suitably N-protected alcohols undergo oxidation to aldehyde followed by Grignard addition of allyl magnesium bromide, TBDMS protection of the homoallylic alcohol and reductive ozonolysis of the olefin to get a primary alcohol which is subject to Fukuyama-Mitsunobu reaction with desire protected peptide. The residue preferences that produce strongest inter-strand H-bonds were explored. The designed 4-carbon covalent HBS was incorporated using this methodology in a Gramicidin-S analogue, its first structural mimic containing only a single turn motif. This HBS model will have wide applications for constraining peptides in a number of secondary structures.

Motivated by the classic works of Charles M. Stein, we focus on developing risk-estimation frameworks for denoising problems in both one-and two-dimensions. We assume a standard additive noise model, and formulate the denoising problem as one of estimating the underlying clean signal from noisy measurements by minimizing a risk corresponding to a chosen loss function. Our goal is to incorporate perceptually-motivated loss functions wherever applicable, as in the case of speech enhancement, with the squared error loss being considered for the other scenarios. Since the true risks are observed to depend on the unknown parameter of interest, we circumvent the roadblock by deriving finite-sample un-biased estimators of the corresponding risks based on Stein’s lemma. We establish the link with the multivariate parameter estimation problem addressed by Stein and our denoising problem, and derive estimators of the oracle risks. In all cases, optimum values of the parameters characterizing the denoising algorithm are determined by minimizing the Stein’s unbiased risk estimator (SURE). The key contribution of this thesis is the development of a risk-estimation approach for choosing the two critical parameters affecting the quality of nonparametric regression, namely, the order and bandwidth/smoothing parameters. This is a classic problem in statistics, and certain algorithms relying on derivation of suitable finite-sample risk estimators for minimization have been reported in the literature (note that all these works consider the mean squared error (MSE) objective). We show that a SURE-based formalism is well-suited to the regression parameter selection problem, and that the optimum solution guarantees near-minimum MSE (MMSE) performance. We develop algorithms for both glob-ally and locally choosing the two parameters, the latter referred to as spatially-adaptive regression. We observe that the parameters are so chosen as to tradeoff the squared bias and variance quantities that constitute the MSE. We also indicate the advantages accruing out of incorporating a regularization term in the cost function in addition to the data error term. In the more general case of kernel regression, which uses a weighted least-squares (LS) optimization, we consider the applications of image restoration from very few random measurements, in addition to denoising of uniformly sampled data. We show that local polynomial regression (LPR) becomes a special case of kernel regression, and extend our results for LPR on uniform data to non-uniformly sampled data also. The denoising algorithms are compared with other standard, performant methods available in the literature both in terms of estimation error and computational complexity. A major perspective provided in this thesis is that the problem of optimum parameter choice in nonparametric regression can be viewed as the selection of optimum parameters of a linear, shift-invariant filter. This interpretation is provided by deriving motivation out of the hallmark paper of Savitzky and Golay and Schafer’s recent article in IEEE Signal Processing Magazine. It is worth noting that Savitzky and Golay had shown in their original Analytical Chemistry journal article, that LS fitting of a fixed-order polynomial over a neighborhood of fixed size is equivalent to convolution with an impulse response that is fixed and can be pre-computed. They had provided tables of impulse response coefficients for computing the smoothed function and smoothed derivatives for different orders and neighborhood sizes, the resulting filters being referred to as Savitzky-Golay (S-G) filters. Thus, we provide the new perspective that the regression parameter choice is equivalent to optimizing for the filter impulse response length/3dB bandwidth, which are inversely related. We observe that the MMSE solution is such that the S-G filter chosen is of longer impulse response length (equivalently smaller cutoff frequency) at relatively flat portions of the noisy signal so as to smooth noise, and vice versa at locally fast-varying portions of the signal so as to capture the signal patterns. Also, we provide a generalized S-G filtering viewpoint in the case of kernel regression. Building on the S-G filtering perspective, we turn to the problem of dynamic feature computation in speech recognition. We observe that the methodology employed for computing dynamic features from the trajectories of static features is in fact derivative S-G filtering. With this perspective, we note that the filter coefficients can be pre-computed, and that the whole problem of delta feature computation becomes efficient. Indeed, we observe an advantage by a factor of 104 on making use of S-G filtering over actual LS polynomial fitting and evaluation. Thereafter, we study the properties of first-and second-order derivative S-G filters of certain orders and lengths experimentally. The derivative filters are bandpass due to the combined effects of LPR and derivative computation, which are lowpass and highpass operations, respectively. The first-and second-order S-G derivative filters are also observed to exhibit an approximately constant-Q property. We perform a TIMIT phoneme recognition experiment comparing the recognition accuracies obtained using S-G filters and the conventional approach followed in HTK, where Furui’s regression formula is made use of. The recognition accuracies for both cases are almost identical, with S-G filters of certain bandwidths and orders registering a marginal improvement. The accuracies are also observed to improve with longer filter lengths, for a particular order. In terms of computation latency, we note that S-G filtering achieves delta and delta-delta feature computation in parallel by linear filtering, whereas they need to be obtained sequentially in case of the standard regression formulas used in the literature. Finally, we turn to the problem of speech enhancement where we are interested in de-noising using perceptually-motivated loss functions such as Itakura-Saito (IS). We propose to perform enhancement in the discrete cosine transform domain using risk-minimization. The cost functions considered are non-quadratic, and derivation of the unbiased estimator of the risk corresponding to the IS distortion is achieved using an approximate Taylor-series analysis under high signal-to-noise ratio assumption. The exposition is general since we focus on an additive noise model with the noise density assumed to fall within the exponential class of density functions, which comprises most of the common densities. The denoising function is assumed to be pointwise linear (modified James-Stein (MJS) estimator), and parallels between Wiener filtering and the optimum MJS estimator are discussed.