Les microalgues autotrophes sont une source prometteuse de biomasse pour des applications aussi variées que l'extraction de molécules, l'alimentation animale et humaine, la production énergétique ou la décontamination environnementale. La production de masse est donc en forte augmentation dans le monde. Cependant, les techniques actuelles pour caractériser l'état physiologique des cellules algales au cours de la croissance sont coûteuses en main d'œuvre et en temps, souvent basées sur du matériel de mesure générique répondant mal au cahier des charges. Elles sont inadaptées à la mesure en ligne.De nouveaux outils doivent donc être développés pour optimiser le pilotage des procédés de culture, en effectuant des mesures rapides de l'état physico-chimique des cellules. La spectroscopie visible (VIS) et proche infrarouge (NIR) se présente comme une solution pratique. De plus des travaux antérieurs ont démontrés que les propriétés spectrales d'absorption et de diffusion des cellules d'algues dans le domaine VIS-NIR sont très corrélées à leur caractéristiques chimiques (pigments) et physiques (tailles, densité des cellules). Les densités de cellules considérées en cultures denses sont très élevées (10^6-10^9 cellules/mL), rendant inévitables les phénomènes de multidiffusion. Cependant ces derniers ont été identifiés comme gênants pour l'extraction de données à partir des spectres mesurés, car ils rendent l'hypothèse de validité de la loi de Beer Lambert fausse. Dans cette thèse nous nous intéressons à l'extraction de données sur la physiologie des cellules algales à partir de mesures spectrales effectuées sur des échantillons denses, non-dilués, directement issus du milieu de culture. Notre approche se décline en plusieurs axes, correspondants aux différentes échelles de description du problème. D'abord, l'échelle de l'échantillon algal global est considérée. Nous en définissons les propriétés spectrales apparentes, et analysons le problème pratique de leur mesure. Nous avons utilisé un montage à double sphères d'intégration et développé un protocole de mesure complet, que nous décrivons. Ensuite, les propriétés spectrales linéaires intrinsèques au milieu algal sont abordées, et nous cherchons à les reliées aux propriétés apparentes de l'échantillon. Pour cela nous utilisons le formalisme de l'équation de transfert radiatif (ETR) donnant une modélisation rigoureuse des phénomènes de multidiffusion à l'œuvre dans les milieux turbides. En pratique, résoudre l'ETR ne peut se faire que par une approximation ou la simulation. Dans nos travaux nous examinons la méthode Adding-Doubling et son inverse, utilisées avec succès par d'autres équipes sur des échantillons turbides de tissus biologiques. En troisième lieu, l'échelle de description de la cellule d'algue individuelle est abordée. AlgaSim, un programme de simulation basé sur la théorie de Mie étendue, a été développé au cours de cette thèse pour modéliser les spectres d'absorption et de diffusion d'une cellule algale décrite par ses paramètres physiologiques, tels que la taille et le poids sec, les proportions des différents matériaux cellulaires, la quantité et la composition des pigments. Ainsi, les liens entre propriétés physiques et chimiques de la cellule et ses propriétés spectrales sont étudiés. Enfin, une méthode complète est proposée pour articuler toutes les échelles de description précédemment examinées. Les liens entre propriétés intrinsèques du milieu algal et les propriétés optiques individuelles des cellules sont cherchés. Les paradigmes développés aux différentes échelles sont ensuite mis bout à bout pour relier la description physiologique des cellules d'algue aux propriétés spectrales apparentes mesurées sur un échantillon donné. La méthode est testée sur des échantillons algaux réels. Les premiers résultats sont prometteurs, démontrant le potentiel opérationnel de la spectroscopie VIS-NIR pour le suivi de procédés de culture dense de microalgues. / Autotrophic microalgae are seen as a promising source of biomass for various applications such as chemicals extraction, animal and human food, energy production and environment cleaning. Consequently, the global mass production of microalgae has largely increased over the last decade. However, the current techniques used for the characterization of the algal cells all along the growth process require time-consuming sample preparation, a large amount of costly, standard instrumentation and cannot usually be performed in situ.New tools are needed to optimize the monitoring of the cultivation process by providing a faster measurement of the microalgal cells physical and chemical states. For this purpose, utilizing visible (VIS) and near infrared (NIR) spectroscopy is looked as a promising solution. Moreover, previous studies demonstrated that the spectral absorption and scattering properties of microalgal suspensions in the VIS-NIR domain depend heavily on the chemical characteristics (pigments) and physical characteristics of the cells (size, density of the cells). In a context of cultivation process, cell density in the culture medium is very high (10^6-10^9 cell/mL) which makes the multi-scattering phenomena significant. However, recent studies have showed that the data extraction from spectroscopic measurements performed on turbid samples is highly complicated by the influence of the scattering phenomena on the spectra, making the classical processing methods based on the assumption of Beer law irrelevant. This thesis addresses the issue of retrieving information about the physiological state of microalgal cells from spectral measurements performed on non-diluted, dense bulk culture media. For this purpose, our approach includes successive guidelines, corresponding to different scales of description. First, the scale of the bulk algal aliquot is considered: the apparent spectral properties are defined, and the practical issue of measuring them with an adapted setup is investigated. In particular, a double-integrating sphere setup, as well as a complete measurement protocol are implemented. Second, the intrinsic linear spectral properties of the dense algal medium are defined, and the links between the intrinsic and apparent spectral properties are investigated. The formalism of the radiative transport equation (RTE) is used for this purpose, as it rigorously models the physical phenomena due to multiple scattering. Solving the RTE must be implemented in practice with an approximation or simulation method. In this work, we investigate in particular the Adding-Doubling method and its inverse, which have been proved to be adapted to the case of highly turbid organic tissues and materials. Third, the scale of an individual algal cell is considered. In this thesis we have developed a simulation program called AlgaSim based of the extended Mie theory, which makes it possible to simulate the spectral absorption and scattering properties of an algal cell described by its physiological characteristics, such as its mean size and dry weight, proportions of different cell materials and pigment quantity and composition. The links between the chemical and physical properties of an algal cell and its spectral properties are thus investigated.Finally, a complete method is proposed to link all the scales of description. In particular, the links between the intrinsic spectral properties of an algal medium and the individual properties of the constitutive cells are considered. By organizing all the paradigms previously investigated, it is possible to implement a complete model linking the physiological description of the constitutive algal cells to the apparent spectral properties measured on a dense culture sample. The method and its inverse are tested on real algal samples. They show promising primary results, proving the operational potential of VIS-NIR spectroscopy for the monitoring of dense algal cultures.

In this work we develop algorithms for the k-Supplier with Outliers problem. In a network, we are given a set of suppliers and a set of clients. The goal is to choose k suppliers so that the distance between every served client and its nearest supplier is minimized. Clients that are not served are called outliers and the number of allowed outliers is given on input. As k-Supplier with Outliers has numerous applications in logistics, we focus on parameters which are suitable for transportation networks. We study graphs with low highway dimension, which was proposed by Abraham et al. [SODA 2010], and low doubling dimension. It is known that unless P = NP, k-Supplier with Outliers does not admit a (3 − ε)-approximation algorithm for any constant ε > 0. The k-Supplier with Outliers problem is W[1]-hard on graphs of constant doubling dimension for parame- ters k and highway dimension. We overcome both of these barriers through the paradigm of parameterized approximation algorithms. In the case of highway dimension, we develop a (1 + ε)-approximation algorithm for any ε > 0 with running time f(k, p, h, ε) · nO(1) where p is the number of allowed outliers, h is the highway dimension of the input graph, and f is some computable function. In the case of doubling dimension, we develop a (1 + ε)-approximation...

Doctor of Philosophy / Department of Mathematics / Charles N. Moore / The main focus of this work is to study the classical Calder\'n-Zygmund theory and its recent developments. An attempt has been made to study some of its theory in more generality in the context of a nonhomogeneous space equipped with a measure which is not necessarily doubling. We establish a Hedberg type inequality associated to a non-doubling measure which connects two famous theorems of Harmonic Analysis-the Hardy-Littlewood-Weiner maximal theorem and the Hardy-Sobolev integral theorem. Hedberg inequalities give pointwise estimates of the Riesz potentials in terms of an appropriate maximal function. We also establish a good lambda inequality relating the distribution function of the Riesz potential and the fractional maximal function in $(\rn, d\mu)$, where $\mu$ is a positive Radon measure which is not necessarily doubling. Finally, we also derive potential inequalities as an application.

Mitochondrial mutations and heteroplasmy have been associated with disease states that result from inadequate cellular energy production. As mitochondrial DNA (mtDNA) encodes many of the polypeptides involved in oxidative phosphorylation (OXPHOS), mtDNA mutations may lower energy production which is required for cell division and sustained ATP synthesis. In order to test the relationship between mtDNA mutations and the rate of cell division, a mammary epithelial cancer cell line, MCF-7, is used as a model. Nine proliferate single cell clones have been isolated from MCF-7. Population doubling times of six single cell clones and the MCF-7 stock have been determined. Clones with distinctly different growth rates were selected for mutational analysis. Growth rates of these clones appeared to be different from each other. Using polymerase chain reaction (PCR) and DNA sequencing, three cases of heteroplasmy have been identified in the mitochondrial genes of the MCF-7 stock and four single cell clones (ATPase C9119T, ND6 T14300G, Cytb G15807A). Heteroplasmy present in the Cytb gene is differs between single cell clones. Differences between the growth rates may be indicative of metabolic variations in these single cell clones. The OXPHOS enzymes encoded by the mutated genes were quantified by standard enzymatic assays. The assays demonstrated significant differences in specific activity between the clones, but were not correlated with mitochondrial heteroplasmy. This thesis determines that the differences in specific activity observed between clones is of nuclear origin.

Mitochondria are the main sites for adenosine triphosphate (ATP) generation within most cells. Structural and functional alterations of mitochondria due to genetic abnormalities of mitochondria can cause respiratory chain dysfunction. In this study, the important role of mitochondria in energy metabolism was determined by comparing the effect of mitochondrial DNA (mtDNA) mutations on growth patterns and oxidative phosphorylation (OXPHOS) enzyme activities of six isolated clones (B5, B12, D4, D9, E1 and E8); as well as the effect of ATP supplement to culture using the slowest growing clone. The isolated clones had shown distinct growth pattern and morphology. The difference in proliferation rates among the clones was ascertained by the doubling times (B5=26.4h. B12=43.2h. D4=25.7h. D9=33.6h. E1=26.9h and E8=28.8h). The clone's slow growth rate was likely the result of mitochondrial mutations in the 16S rRNA gene, ND1, ND4, ND6 and COX III. Five heteroplasmic mutations were found in clone B12 (G2480T, C2513G, A2520T, C9527T and C14263G), one heteroplasmic mutation in clone D9 (A4137G) and one homoplasmic mutation in clone D4 (C11496). The mutations in clone B12 appeared to be deleterious to the cell by disrupting mitochondrial OXPHOS activities and reducing energy output. Additionally, extracellular ATP supplement to OXPHOS deficient clone B12 facilitated cell growth and enhances the gene expression. Increased expression of mtDNA-encoded respiratory chain complexes observed in clone B12 compared to clone D4 may reflect mitochondrial genomic adaptation to perturbations in cellular energy requirements. The stimulation of mitochondrial biogenesis may be a cellular response in compensation for defects in OXPHOS associated with mtDNA mutations. My data support the hypothesis that the variability in functional manifestations of mtDNA is attributed to the nature of the mutation, number of mutation and the gene specifically affected. These results will help to further our understanding of the relationship between mitochondrial mutation and cellular function.

Doctor of Philosophy / Department of Mathematics / Diego Maldonado / Originally introduced in 1961 by Carl Gustav Axel Harnack [36] in the context of harmonic functions in R[superscript]2, the so-called Harnack inequality has since been established for solutions to a wide variety of different partial differential equations (PDEs) by mathematicians at different times of its historical development. Among them, Moser's iterative scheme [47-49] and Krylov-Safonov's probabilistic method [43, 44] stand out as pioneering theories, both in terms of their originality and their impact on the study of regularity of solutions to PDEs. Caffarelli's work [12] in 1989 greatly simplified Krylov-Safonov's theory and established Harnack's inequality in the context of fully non-linear elliptic PDEs. In this scenario, Caffarelli and Gutierrez's study of the linearized Monge-Ampere equation [15, 16] in 2002-2003 served as a motivation for axiomatizations of Krylov-Safonov-Caffarelli theory [3, 25, 57]. The main work in this dissertation is a new axiomatization of Krylov-Safonov-Caffarelli theory. Our axiomatic approach to Harnack's inequality in spaces of homogeneous type has some distinctive features. It sheds more light onto the role of the so-called critical density property, a property which is at the heart of the techniques developed by Krylov and Safonov. Our structural assumptions become more natural, and thus, our theory better suited, in the context of variational PDEs. We base our method on the theory of Muckenhoupt's A[subscript]p weights. The dissertation also gives an application of our axiomatic approach to Harnack's inequality in the context of infinite graphs. We provide an alternate proof of Harnack's inequality for harmonic functions on graphs originally proved in [21].

Thesis advisor: Solomon Friedberg / Kazhdan and Patterson constructed generalized theta representations on covers of general linear groups as multi-residues of the Borel Eisenstein series. For the double covers, these representations and their (degenerate-type) unique models were used by Bump and Ginzburg in the Rankin-Selberg constructions of the symmetric square L-functions for GL(r). In this thesis, we study two other types of models that the theta representations may support. We first discuss semi-Whittaker models, which generalize the models used in the work of Bump and Ginzburg. Secondly, we determine the unipotent orbits attached to theta functions, in the sense of Ginzburg. We also determine the covers for which these models are unique. We also describe briefly some applications of these unique models in Rankin-Selberg integrals for covering groups. / Thesis (PhD) — Boston College, 2017. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Mathematics.

The aim of this paper is to validate a dataset collected by means of production experiments which are part of the Questionnaire on Information Structure. The experiments generate a range of information structure contexts that have been observed in the literature to induce specific constructions. This paper compares the speech production results from a subset of these experiments with specific claims about the reflexes of information structure in four different languages. The results allow us to evaluate and in most cases validate the efficacy of our elicitation paradigms, to identify potentially fruitful avenues of future research, and to highlight issues involved in interpreting speech production data of this kind.

In this paper, doubling in Russian Sign Language and Sign Language of the Netherlands is discussed. In both sign languages different constituents (including verbs, nouns, adjectives, adverbs, and whole clauses) can be doubled. It is shown that doubling in both languages has common functions and exhibits a similar structure, despite some differences. On this basis, a unified pragmatic explanation for many doubling phenomena on both the discourse and the clause-internal levels is provided, namely that the main function of doubling both in RSL and NGT is foregrounding of the doubled information.

This thesis proposes that an investigation into the phenomenon of doubling may engage architecture with a type of desire that has deep rooted connections with the complexities of human nature, with the very human condition of desiring to know who/what/where/when/how we are. It proposes that an experience of doubling is suggestive of a specific kind of affective space that tests this relationship, expanding into the interval we have formed between our body, its being and space. The proposal is to explore the material, spatial, and psychological characteristics of such a phenomenon - to understand the virtual space created through this doubling and its architectonic characteristics. The design ambition of this thesis is to construct an architectural fiction that engages with this doubling. If architecture has the capacity to embody the ambitions and anxieties of society, the work produced attempts to invoke, through choreographed doublings manifested by the movement of figure and light through constructions in time, that human condition of desire that is concerned with finding/defining itself in the unknown, not to provide an answer for what the unknown is, but to engage with its enigmatic nature. By engaging in the protean dynamics of doubling and desire, this thesis attempts to poeticize the interval between the body and its built environment.