Дисертації з теми "Active mixtures"

Thesis: Nav. E., Massachusetts Institute of Technology, Department of Mechanical Engineering, May, 2020
Thesis: S.M., Massachusetts Institute of Technology, Department of Mechanical Engineering, May, 2020
Cataloged from the official PDF of thesis.
Includes bibliographical references (pages 75-78).
In a step towards the level of autonomy seen in humans, this work attempts to emulate a high level and low level approach to world representation and short term adaptation. Specifically, this work demonstrates an implementation of robotic perception that transforms stereo camera and LIDAR sensor data into a sparse map of semantic objects and a locally consistent flexible occupancy grid. This provides a topological representation for grouping objects into higher level classes and a geometric map for traditional planning. Additionally, a reactive dynamic window obstacle avoidance system is shown to quickly plan short term trajectories that avoid both static and dynamic objects while progressing towards a goal. To combine computational efficiency with the robust advantages of multimodal inference, this work uses Semantic Max Mixture factors to approximate multimodal belief in a manner compatible to nonlinear least squares solvers. Experimental results are presented using a RACECAR mobile robot operating in several hallways of MIT, using AprilTags as surrogates for objects in the Semantic Max Mixtures Algorithm. Future work will seek to further integrate the components to create a closed-loop active semantic navigation and mapping algorithm.
by David P. Baxter.
Nav. E.
S.M.
Nav.E. Massachusetts Institute of Technology, Department of Mechanical Engineering
S.M. Massachusetts Institute of Technology, Department of Mechanical Engineering

Les systèmes vivants consomment continuellement de l'énergie et ont ainsi accès à des états hors-équilibre qui leur confèrent des propriétés fascinantes. L'étude physique des systèmes vivants repose souvent sur des analogies avec des systèmes de la matière molle, tels que les colloïdes. Dans cette thèse, nous investiguons deux systèmes colloïdaux bidimensionnels hors l'équilibre thermodynamique, qui présentent des phénomènes d'auto-assemblage, de viscoélasticité, de transitions de phase et de ségrégation semblables à ceux de certains systèmes biologiques. Dans la première partie de la thèse, nous étudions expérimentalement et théoriquement la dynamique des agrégats de colloïdes paramagnétiques sous un champ magnétique tournant, qui agit comme une source constante d'énergie. Nous caractérisons la dynamique de rotation des agrégats, que nous expliquons par un modèle théorique qui décrit l'émergence de propriétés viscoélastiques collectives. Le modèle capture avec succès la dépendance entre la vitesse de rotation mesurée et les caractéristiques des particules, des agrégats et du champ, et il fournit une estimation de la viscoélasticité de l'agrégat. Nous étendons notre étude au cas des agrégats binaires de deux types de colloïdes, qui ont des tailles et des susceptibilités magnétiques différentes. La dynamique des agrégats en fonction des compositions est correctement décrite par notre modèle théorique généralisé. Nous caractérisons également l'évolution de la structure de ces agrégats binaires, qui rappelle la ségrégation entre deux liquides non miscibles. Motivés par les phénomènes d'étalement des agrégats vivants, nous étudions ensuite le désassemblage d'un agrégat de colloïdes en réponse à un changement du champ magnétique externe, par expérience et théorie. Dans la deuxième partie de la thèse, nous étudions un mélange binaire de colloïdes de Lennard-Jones actifs et passifs, caractérisés par deux températures effectives différentes, ce qui correspond à une différence d'activité scalaire. Nous effectuons des simulations de dynamique moléculaire où les deux types de colloïdes sont couplés à deux thermostats différents. Nous nous intéressons à deux systèmes de référence à l'équilibre thermodynamique : un mélange homogène et un système interfacial gaz-liquide. Nous amenons ces systèmes à des états stationnaires hors-équilibre en introduisant une différence de température effective entre les deux espèces, et nous étudions systématiquement les changements de structure et propriétés qui en résultent. Pour le système homogène, l'introduction d'une différence d'activité entre les deux espèces déplace le mélange du solide vers l'état liquide et le rend plus déformable que ce qui correspondrait à la température effective moyenne du système. Lorsque la différence d'activité dépasse un certain seuil, des phénomènes de ségrégation sont observés. Pour le système interfacial, nous étudions l'effet de l'activité sur une interface gaz-liquide pré-existante entre deux espèces séparées. Nous constatons qu'une différence d'activité élevée induit la formation de nouvelles interfaces solide-liquide, tandis qu'une différence faible déstabilise les interfaces liquide-gaz préexistantes. De plus, la combinaison d'une interface préexistante avec une activité différentielle conduit à une cristallisation partielle et donc à une coexistence de trois phases (solide, liquide et gaz). Les résultats obtenus dans ces systèmes idéalisés pourraient guider notre compréhension et mettre en évidence des mécanismes physiques présents dans les systèmes biologiques, où des comportements dynamiques similaires sont observés
Living systems generally operate in non-equilibrium states by continuously consuming energy, thus exhibiting rich collective dynamics and properties. Physical investigations often rely on analogies with model systems in soft matter, such as colloids. In this thesis, we develop two colloidal model systems that operate in non-equilibrium states and exhibit interesting phenomena similar to those of certain biological systems, such as self-assembly, viscoelasticity, phase transitions, and segregation. In the first part of this thesis, we study experimentally and theoretically the dynamics of two-dimensional clusters of paramagnetic colloids under a time-varying magnetic field. Due to the continuous energy input by the rotating field, these self-assembled clusters are at a dissipative non-equilibrium state. We experimentally characterize the dynamics of cluster rotation and we develop a theoretical model to explain the observations by the emergence of collective viscoelastic properties. The model successfully captures the observed dependence on particle, cluster, and field characteristics, and it provides an estimate of cluster viscoelasticity. We extend our study to the case of binary clusters of colloids of two different sizes and magnetic susceptibilities. The composition dependence of the rotation dynamics is successfully captured by a generalization of our theoretical model. We also investigate the evolution of the internal distribution of the two particle types, reminiscent of segregation in a drop of two immiscible liquids, and the effect of such structure on the rotation dynamics. Next, we study cluster disassembly in response to a change in the external field. The experimentally observed disassembly dynamics are successfully described by a model, which moreover provides an estimate of the particle-substrate friction coefficient. In the second part of the thesis, we investigate a two-dimensional binary mixture of active and passive Lennard-Jones colloids, characterized by different degrees of scalar activity, modeled by an effective temperature difference. We perform molecular dynamics simulations of this system using two different thermostats. We consider two equilibrium reference systems: a homogeneous system and a gas-liquid interfacial system. We drive these systems out-of-equilibrium by increasing the effective temperature difference and we systematically investigate the effect on their behaviors and properties. For the homogeneous system, our results indicate that the presence of differential activity shifts the mixture from solid towards the liquid state and renders it more deformable than a homogeneous state at the average temperature. The binary mixture remains homogeneous for moderate activity difference between the two species, and segregation arises for a sufficiently large activity difference. For the interfacial system, we investigate the effect of activity on a pre-existing gas-liquid interface between two separated species. We find that a high activity difference induces the formation of new solid-liquid interfaces, whereas a low difference destabilizes pre-existing liquid-gas interfaces. Moreover, the combination of a pre-existent interface with differential activity leads to partial crystallization and thus to triple phase coexistence (solid, liquid, and gas), which is observed over a wide range of differential activities. Our findings from these idealized systems could guide our understanding and point to certain physical mechanisms at play in biological systems, where similar dynamical behaviors are observed

This thesis attempts to provide a deeper understanding of the effect of mineral fillers on the aging of bitumen with and without the presence of moisture in the mixture. More specifically, a chemical and mechanical performance characterization of mineral fillers containing hydrated lime was carried out, deepening the issue of degradation and carbonation in limestone following oxidative aging. Six different mineral fillers have been used in this research; the fillers differed with respect to the amount of active hydrated lime. The mixtures of bitumen-mineral fillers were prepared according to a single design protocol. The resulting mastics together with the neat bitumen were subjected to accelerated aging in the laboratory by means of the Pressure Aging Vessel (PAV). The ageing protocols differed with regard to the gas that was used and the presence of humidity. After each conditioning protocol, the samples were tested by using Dynamic Shear Rheometer (DSR) and Fourier Transfer Infrared spectrometer (FTIR). DSR was used to determine the rheological properties of materials, such as relaxation, fatigue and stiffness. FTIR was used to study the chemical composition of fillers and mastics before and after conditioning. The FTIR measurements were further used to develop a methodology that enables the quantification of the degradation of hydrated lime due to moisture and ageing effects.

The work herein investigates the surface active properties of short peptides and their interactions with conventional surfactants. Short peptides can be designed to mimic the structures of conventional surfactants such as SDS and C12TAB. Such peptide structures include V6K peptide, which are attractive in many fields and applications as they can be more biocompatible, biodegradable and environmentally friendlier substitutes to harsh surfactants. Similar peptide structures can also be found naturally occurring in proteins, such as silk fibroin, and can then be liberated by breaking down the protein into its constituent peptides. The interaction of these peptides with conventional surfactants at the air-liquid and solid-liquid interface have not been investigated before. The adsorption behaviour and structures formed at the solid-liquid interface were examined using Ellipsometry and Neutron Reflection.

L'amélioration de la solubilité est un aspect critique dans la formulation et le développement de nouvelles molécules thérapeutiques. Pour surmonter les défis associés à une faible solubilité, les chercheurs ont évalué de nombreuses stratégies, dont l'utilisation de cyclodextrines et de cosolvants. Cette dernière approche est une technique simple et efficace, dans laquelle des solvants organiques sont utilisés pour améliorer la solubilité des composés peu solubles dans l'eau. Ces dernières années, les solvants eutectiques profonds (DESs) ont émergé comme une alternative abordable et verte comparée aux solvants organiques, d'autant plus qu'ils sont très prometteurs pour la solubilisation de molécules hydrophobes. Plus récemment, des DESs à base de cyclodextrines (CDs) ont été introduits sous le nom de "solvants eutectiques profonds supramoléculaires"(SUPRADESs). Les cyclodextrines (CDs) sont des molécules cages, réputées pour leur capacité à améliorer la solubilité et la stabilité des principes actifs encapsulés dans leur cavité. Cette étude visait à évaluer le potentiel de DESs et de SUPRADESs pour une application dans des préparations pharmaceutiques. À cette fin, un panel de DESs et de SUPRADESs sélectionnés a été d'abord préparé et caractérisé. La calorimétrie différentielle à balayage (DSC) et l'analyse thermogravimétrique (TGA) ont démontré que les solvants étaient liquides sur une large plage de température et stables jusqu'à 100°C. Les mesures de densité et de viscosité ont montré que les propriétés des DESs pouvaient être ajustées en fonction de leur composition. Les spectroscopies infrarouges (IR) et de résonance magnétique nucléaire (RMN) ont fourni des preuves de la formation de liaisons hydrogène au sein des solvants préparés. Ensuite, la solubilité et la stabilité d'une série de principes actifs (APIs) peu solubles dans l'eau ont été évaluées. Les solvants ont montré une amélioration significative de la solubilité et une bonne stabilité après une année de stockage. L'effet de l'ajout d'eau sur le pouvoir solubilisant a également été évalué. Ces expériences ont mis en évidence l'avantage des SUPRADESs par rapport aux DESs car ils se sont révélés plus résistants à l'effet de dilution. Ce comportement a été attribué à la formation de complexe d'inclusion CD/API, comme le prouvent les études RMN. Enfin, les expériences de libération de médicaments ont montré que l'utilisation des DESs et des SUPRADESs entraînait une augmentation des taux de dissolution par rapport au médicament intact. Dans l'ensemble, ces résultats soulignent le pouvoir des DESs et des SUPRADESs à être utilisés comme solvants dans les formulations pharmaceutiques
Solubility enhancement is a critical aspect in the formulation and development of novel drug molecules. To overcome challenges associated with poor solubility, formulation scientists have explored numerous strategies, among them the use of cyclodextrins and cosolvents. The latter approach is a simple and effective method, where organic solvents are used to enhance the solubility of poorly water-soluble compounds. In recent years, deep eutectic solvents (DESs) have emerged as a cheap and green alternative to organic solvents, showing great promise for the solubilization of hydrophobic molecules. More recently, DESs based on cyclodextrins (CDs) have been introduced under the name "supramolecular deep eutectic solvents" (SUPRADESs). Cyclodextrins (CDs) are cage molecules renowned for their ability to enhance the solubility and stability of drug molecules entrapped inside their cavity.This study aimed to evaluate the potential of DESs and SUPRADESs for use in pharmaceutical preparations. To this end, a panel of selected DESs and SUPRADESs were first prepared and characterized. Differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) demonstrated that the solvents are liquid over a broad temperature range and stable up to 100°C. Density and viscovity measurements showed that DESs' properties can be tuned depending on their composition. Infrared (IR) and nuclear magnetic resonance (NMR) spectroscopies provided evidence of hydrogen bonds formation in the prepared solvents. Further, the solubility and stability of a series of poorly water-soluble active pharmaceutical ingredients (APIs) were evaluated. The solvents displayed significant solubility enhancement and good stability after a year of storage. In addition, the effect of water addition on the solubilizing potential was evaluated. These experiments highlighted the advantage of using SUPRADESs over DESs, since they were revealed to be more resistant to dilution effect. This was attributed to the formation of CD/API inclusion complex, as proved by NMR studies. Finally, drug release experiments showed that the use of DESs and SUPRADESs resulted in increased dissolution rates compared to the solid drug. Overall, these findings support the potential of DESs and SUPRADESs for being used as solubilizing vehicles in phamaceutical formulations

La matière active englobe les systèmes hors d'équilibre dont les constituants microscopiques exercent des forces d'auto-propulsion non conservatives sur leur environnement. L'auto-organisation des unités actives en structures complexes est observée à toutes les échelles dans le monde vivant, des écosystèmes bactériens aux groupes d'oiseaux. De plus, ces dernières années, les physiciens et les chimistes ont été capables de concevoir des particules synthétiques capables d'auto-propulsion, telles que les colloïdes de Janus auto-phorétiques ou les rollers de Quincke, ouvrant ainsi la voie à la réalisation de matériaux actifs intelligents. À cet égard, comprendre le lien entre la dynamique microscopique des particules actives et leurs propriétés à grande échelle est un problème crucial tant pour la biologie que pour l'ingénierie bio-mimétique. Dans ce manuscrit, nous comblons cette lacune pour un certain nombre de systèmes actifs scalaires, i.e. des systèmes actifs dont le seul mode hydrodynamique à grande échelle est le champ de densité. En particulier, une grande partie du manuscrit est consacrée aux systèmes actifs à plusieurs composants, ou mélanges actifs, dont l'étude est pertinente pour obtenir des descriptions plus réalistes des communautés biologiques: des écosystèmes animaux aux colonies bactériennes, la polydispersité est omniprésente dans les systèmes vivants. Le manuscrit est structuré comme suit. Dans le chapitre 1, nous présentons une revue méthodologique sur les techniques de coarse-graining dans les systèmes actifs scalaires. Ces méthodes sont ensuite appliquées dans le chapitre 2 pour caractériser le comportement à grande échelle de particules actives en présence de différents mécanismes tactiques. La deuxième partie de la thèse est consacrée aux comportements collectifs dans les systèmes actifs scalaires en interaction. Dans le chapitre 3, nous étudions la régulation de la motilité non réciproque dans les mélanges binaires de particules actives, révélant l'impact de la non-réciprocité microscopique sur l'organisation macroscopique du système. Suivant cette ligne, dans le chapitre 4, nous considérons un écosystème bactérien où un grand nombre d'espèces coexistent ensemble, révélant comment une infime régulation de la motilité aléatoire peut suffire à favoriser la formation de communautés bactériennes distinctes. Pour conclure, dans le chapitre 5, nous passons de la matière biologique à la matière active synthétique, en étudiant un modèle de bâtonnets de Quincke autopropulsés. En particulier, nous montrons comment ces particules subissent une transition de condensation arrêtée, où la compétition entre quorum sensing et répulsion stérique est cruciale pour stabiliser les phases coexistantes
Active matter encompasses out-of-equilibrium systems whose microscopic constituents exert non-conservative self-propulsion forces on their environment. The self-organization of active units into complex structures is observed at all scales in the living world, from bacterial ecosystems to flocks of birds. Furthermore, in recent years, physicists and chemists have been able to engineer synthetic particles capable of self-propulsion, such as self-phoretic Janus colloids or Quincke rollers, thus paving the way towards the realization of smart active materials. In this regard, understanding the link between the microscopic dynamics of active particles and their large-scale properties is a crucial problem for both biology and bio-inspired engineering. In this manuscript, we bridge this gap for a number of scalar active systems, i.e. active systems where the only large-scale hydrodynamic mode is the conserved density field. In particular, a large part of the manuscript is devoted to multi-component active systems---or active mixtures---whose study is relevant to achieve more realistic descriptions of biological communities: from animal ecosystems to bacterial colonies, polydispersity is ubiquitous in living systems. The manuscript is structured as follows. In Chapter 1 we provide a methodological review of coarse-graining techniques in scalar active systems. These methods are then applied in Chapter 2 to characterize the large-scale behaviors of non-interacting active particles with different tactic mechanisms. The second part of the thesis is devoted to collective behaviors in interacting scalar active systems. In Chapter 3 we study the impact of non-reciprocal motility regulation in binary mixtures of active particles, and show how the microscopic non-reciprocity affects the macroscopic organization of the system. Following this line, in Chapter 4 we consider a bacterial ecosystem where a large number of species coexist, revealing how weak, random motility regulation can be sufficient to promote the formation of distinct bacterial communities. To conclude, in Chapter 5 we shift from biological to synthetic active matter, studying a model for self-propelled Quincke rods. In particular, we show how these rods can undergo an arrested condensation transition, where the interplay between quorum-sensing and steric repulsion is crucial to stabilize the coexisting phases

In this thesis, the population pharmacokinetics of telapristone and its active metabolite, CDB-4453 was evaluated using nonlinear mixed effects modeling (NONMEM®). A two-compartment (parent) one compartment (metabolite) mixture model with first order absorption and elimination adequately described the pharmacokinetics of telapristone and CDB-4453. For the Phase I/II pharmacokinetic analysis (effect of renal and hepatic impairment), telapristone was rapidly absorbed with an absorption rate constant (Ka) of 1.26 h-1. Moderate renal impairment resulted in a 74% decrease in Ka. Population estimates for oral clearance (CL/F) for the high and low clearance groups were 11.6 L/h and 3.34 L/h, respectively. Twenty-five percent of the subjects were allocated to the high clearance group. Apparent volume of distribution for the central compartment (V2/F) was 37.4 L, apparent inter-compartmental clearance (Q/F) was 21.9 L/h, and apparent peripheral volume of distribution for the parent (V4/F) was 120 L. The ratio of the fraction of telapristone converted to CDB-4453 to the distribution volume of CDB-4453 (Fmetest) was 0.20/L and apparent clearance of the metabolite (CLM/F) was 2.43 L/h. For the pharmacokinetic analysis evaluating the effect of food; food decreased the Ka of telapristone (Ka for the fed and fasted state was 0.467 and 5.06 h-1, respectively). Population estimates of the high and low CL/F groups were 12.0 L/h and 3.15 L/h, respectively. Thirty-one percent of the subjects were allocated to the high clearance group. V2/F, Q/F and V/4 and Fmetest were 52.8 L, 7.53 L/h, 84.8 L and 0.193/L, respectively. CLM/F was 2.10 L/h. An external validation was performed using the final parameter estimates from the pooled pharmacokinetic analysis (effect of renal and hepatic impairment and the effect of food). From this pharmacokinetic analysis, Ka for the fed and fasted state was 0.299 and 2.35 h-1, respectively. Population estimates for the high and low CL/F groups were 11.6 L/h and 3.22 L/h, respectively. The percentage of subjects allocated to the high clearance group was 29%. V2/F, Q/F, V/4 and Fmetest were 52.8 L, 11.6 L/h and 93.8 L and 0.186/L, respectively. CLM/F was 2.23 L/h. The final model did not meet the requirement for adequate predictability using the external validation dataset. However, the external validation dataset only included samples with limited early time points. Because of the limited sampling times, it is difficult to make a conclusion about the overall adequacy of the model. An external validation dataset with more extensive sampling will be needed in order to better assess the predictability final model. This is the first comprehensive review of the pharmacokinetics of telapristone and CDB-4453.

We hypothesize that South African medicinal plants contain compounds that can act in synergism with synthetic antifungal compounds. Four fungicides - Sporekill&trade
, Rovral&trade
, Terminator&trade
and Teldor&trade
at doses 0.1, 0.2, 0.4 and 0.8 mL L-1 and plant species Galenia africana, Elytropappus rhinocerotis and Tulbaghia violacea were tested aloneand in different combinations for their potency (efficacy) on radial growth inhibition of Botrytis cinerea strains on potato dextrose plates. Four doses of plant extract for each of the respective plant species were used. A total of 48 combinations were tested for each strain. Mixtures of plant extracts were far more effective in controlling strains compared to the individual components alone, representing significant levels of in vitro synergistic interactions. Combinations of these components represent an attractive future prospect for the development of new management strategies for controlling B. cinerea. Since the in vitro tests of these mixtures showed inhibitory activity, the mixtures were tested for activity in assays on Granny Smith apples. In vitro tests can be used to screen mixtures to obtain information on their inhibitory activity on a pathogen, however, the environmental conditions of the fruit and the ability of the pathogen to grow into the fruit cannot be simulated in vivo. A series of two-fold doses of medicinal plant extracts were combined with fungicides to conduct decay inhibition studies. The incidence of gray mold was significantly reduced by mixtures of plant extracts and fungicides. Under conditions similar to those in commercial storage, a drench treatment with G. africana and Rovral&trade
significantly (p=0.05) inhibit gray mold on the apples and was more effective than the plant extract and fungicide alone. The treatments exerted synergistic effects and were markedly better than the components applied alone. The wound colonization assay was used for optimal decay control. In a drench, much higher volumes of the treatments are used to ensure that the components of the suspension are deposited evenly over the entire fruit surface. Drenching of fruit to apply other chemicals is an established practise in the pome (fleshy) fruit industry, and simplifies the commercial application of the mixtures, as no additional infrastructure at commercial packing houses will be required. This approach not only makes it possible to reduce fungicide concentrations while maintaining adequate decay control, but also ensures a reduction of the chemical residue on the fruit.

Exposure of the embryo to environmental chemicals (pesticides, air and water pollutants) can result in congenital malformations or developmental defects such as oro-facial cleftings. Unfortunately, the human embryo is not usually exposed to a single substance, but to many substances simultaneously. Despite the efforts in elucidating mechanism of action (MoA) of substances that perturb the normal embryonic development, only a small part of involved pathways have been understood to date (Giavini and Menegola, 2004). This is why, evaluating the toxicity of mixtures of multiple chemicals is one of the major objectives of today’s toxicology despite the effect of exposure to a mixture is still difficult to understand. To arrive in the future to the creation of a realistic overall picture of human exposure to mixtures, the development of integrated approaches between in vitro and in silico techniques and computational systems biology, able to predict the effects of mixtures starting from the concentrations of their individual components, will be essential. Recent studies suggest that the similarity of molecular initiating events (MIEs) is not an essential requirement to induce additive effects, because mixtures composed of chemicals with different MIE can exhibit mixture effects too, probably acting on the same biological pathway and contributing to the same adverse outcome (EFSA, 2013). This is in recognition of emerging evidence that biological effects can be similar, although the molecular details of toxicological mechanisms may profoundly differ in many respects (Kortenkamp, 2007). Considering the previously reported data, this could be the case of embryonic co-exposure to fluconazole (FLUCO) and ethanol (Eth). Both, in fact, lead to the same adverse outcome (AO), craniofacial malformations, both after in utero and in vitro exposure. The two molecules are able to induce cranio-facial defects (in embryos visible as cranio-facial abnormalities), probably acting on the same Adverse Outcome Pathway (AOP) altering, with different MIEs, the biological event cascade regulated by the morphogen retinoic acid (RA). The specific aim of this PhD project was to investigate this hypothesis through the development of an in silico model, useful to simulate and predict the effects on embryo development after co-exposure to substances with independent MoAs but acting on the same biological pathway and potentially contributing to the same adverse outcome (cranio-facial malformations). The in silico model was based on experimental data and validated by in vitro experiments. For this purpose, the project was divided into three parts. In the first part, we evaluated the effects of the molecules on post-implantation rat embryos cultures, using the in vitro technique WEC (Whole Embryo Culture). Embryos were cultured in presence of increasing concentration of RA (0.025-0.0375-0.05-0.125-0.25 µM), to increasing concentrations of Eth (17-42.5-85-127 mM), to increasing concentrations of FLUCO (62.5-125-250-500 µM). Specific and concentration related abnormalities at the level of the branchial arches (reductions or fusions) were observed after exposure to single Eth or FLUCO and were comparable to those elicited by RA. These results suggest a common AO for Eth, FLUCO and RA. Embryos were then co-exposed to binary mixtures of FLUCO and Eth. To better characterize the contribution of each component to the observed effects, the “fixed + moving” approach was applied: embryos were exposed to the no effect concentration (NOAEL) of one chemical (“fixed”) and increasing concentrations of the other chemical (“moving”). A significant enhancement of teratogenic effects was observed after co-exposure to FLUCO and Eth in comparison to the single exposure. The mixture between the two NOAELs was effective too, inducing almost 40% of branchial arch abnormalities. These data suggest the presence of a cumulative effect in mixture, probably due to the capability of both molecules to perturb RA endogenous concentrations in specific tissues (the precursors of cranio-facial skeletal tissues, originated in the embryonic hindbrain). This theory could be explained considering the ability of Eth to induce alcohol-dehydrogenases (including ADH7, the embryonic enzyme involved in RA synthesis) and the inhibitory effects of FLUCO on cytochromes p450 (including CYP26, involved in embryonic RA degradation). In the second part of the project, we evaluated these hypothetical mechanisms inducing the Eth-FLUCO mixture effects through the development of an in silico tool, able to simulate both the formation of the physiological RA gradient in the rat embryo hindbrain and its perturbation after exposure to FLUCO, Eth and to their binary mixtures. The obtained system biology model, developed using an integrated approach combining mathematical modelling, molecular docking and in vitro experiments, seems to be reasonably predictive for the mixture’s effects, confirming the accuracy of the hypothesized pathogenic pathway. Experimental data and model predictions, in fact, showed a promising agreement. The model, in spite of its limitations, could have many potential mechanistic or predictive applications for the study of risk assessment. However, since the model is based on experimental data obtained in mammals, the last part of the project was aimed to evaluate alternative animal models. In the third part of the project, the evaluation of the effects after co-exposure to FLUCO and Eth were performed using the ascidian Ciona intestinalis embryo model as a new alternative teratological screening test (AET, Ascidian Embryo Teratogenicity assay). An ascidian species was selected because Ascidiacea represent the sister group of Vertebrates. For this purpose, C. intestinalis embryos were exposed to Eth alone (1.7-8.5-17-42.5-85 mM) to FLUCO alone (7.8-15.75-31.5-250 µM), or co-exposed to binary mixtures of FLUCO and Eth until the larval stage, applying the fix + moving protocol. Specific and concentration related abnormalities at the level of the anterior structures were elicited by Eth or FLUCO, and were comparable to those described in literature after RA exposure. A significant enhancement of the general teratogenicity was observed after co-exposure to FLUCO and Eth in comparison to the single exposure, suggesting the presence of a mixture effect induced by FLUCO and Eth also in this model. These results, similar to those observed in the WEC model, encourage the use of AET as a complementary alternative method for embryotoxicity studies on mixtures. The possibility to translate data obtained in this model in our in silico model is still to evaluate. In conclusion, our data suggest that: 1. the integrated use of data from in vitro and in silico approaches used in this study support the hypothesis that embryonic exposure to FLUCO and Eth can lead to the same AO (craniofacial abnormalities) acting with different MIEs but both converging on the same AOP by altering the RA production (Eth) and the RA catabolism (FLUCO); 2. the hypothesis that substances with different MoAs but acting on the same pathway could produce an additive effect also at concentrations considered not effective is supported; 3. the obtained results highlight the potential additive effect that could occur after exposure to azoles and ethanol, suggesting a precautionary position in alcohol consumption during azoles exposure in pregnancy. The overall view of the obtained results support the need of a cumulative risk assessment not only for chemicals grouped on the base of similarities in chemical structure or derived from mechanistic considerations but also for chemicals differently acting on the same biological pathway.

Cette thèse de doctorat évalue le potentiel de la croissance épitaxiale à basse température (200-300°C) par dépôt chimique en phase vapeur assisté par plasma à partir de SiF4/H2/Ar pour la formation de l’émetteur dans des cellules solaires de type nPERT. La première partie concerne l’identification et l’optimisation des conditions de dépôt pour réaliser des couches épitaxiées faiblement contraintes avec une interface epi/wafer de bonne qualité. La perte d’épitaxie a également été étudiée et nous avons mis en évidence que la formation de macles au cours de la croissance était responsable de la dégradation de la cristallinité. Ensuite, l’étude des mécanismes de croissance a été menée et l’analyse des phases initiales de croissance a permis d’identifier un mode de croissance de type Volmer-Weber.Les conditions de dépôt ont ensuite été transférées à un réacteur PECVD semi-industriel de 6 pouces. Les problèmes d’homogénéité et de vitesse de croissance ont été abordés par le design d’une nouvelle « shower head » grâce aux simulations d’écoulement du gaz. Des couches épitaxiées dopées bore avec un dopage de type p de 4.1019 cm-3 et une efficacité de dopage jusqu’à 70% ont ainsi été fabriquées à seulement 300°C. La vitesse de croissance dans ces conditions atteint 1.1 Å/s, i.e. 15 fois plus rapide que les premiers résultats obtenus. Enfin, la passivation des couches épitaxiées a été étudiée et un temps de vie de 160 μs a été obtenu sur des couches intrinsèques de 200 nm d’épaisseur passivées avec 10 nm d’oxyde d’aluminium
This doctoral work aimed to assess the potential of low-temperature (200-300°C) epitaxy by plasma-enhanced chemical vapor deposition (PECVD) using SiF4/H2/Ar gas mixtures for the emitter formation in nPERT solar cells. The first part of this PhD thesis concerned the identification and the optimization of the process conditions to perform lowly strained intrinsic epi-layers with a smooth epi/wafer interface. We also investigated the causes of epitaxy breakdown and found out that a twinning-induced mechanism was responsible. Subsequently we focused on the growth mechanisms by studying the initial stages of growth and a Volmer-Weber growth mode has been highlighted. Finally, the process conditions for intrinsic epitaxy were transferred from a researchPECVD reactor to a 6 inch semi-industrial one. Inhomogeneity and growth rate issues have been tackled by fluid dynamics simulations resulting in the design of a new shower head. Boron-doped epi-layers grown at 300°C with an as-deposited hole concentration of 4.1019 cm-3 and a doping efficiency up to 70 % have been achieved keeping a low mosaicity and a low variation of the lattice parameter. The growth rate in these conditions reached 1.1 Å/s, i.e 15 times higher than what obtained at the beginning of this PhD for boron-doped epi-layers. Finally, the passivation of epitaxial layers has been investigated and lifetimes up to 160 μs for a 200 nm thick intrinsic layer passivated with

Les phycotoxines lipophiles sont des métabolites secondaires produits par certaines espèces phytoplanctoniques. Elles s'accumulent dans les mollusques filtreurs et peuvent provoquer une intoxication chez l'homme avec une grande variété de symptômes. Ce travail s’est attaché à mieux connaitre leur devenir chez l’homme et leurs effets après ingestion en apportant des données sur leur absorption intestinale et leur métabolisme hépatique puisque ces phénomènes affectent la quantité de toxine circulant dans l’organisme et donc la génération d’effets toxiques. En outre, plusieurs phycotoxines se retrouvent parfois simultanément dans les coquillages alors que les effets de ces mélanges sont encore méconnus. Quatre phycotoxines lipophiles, l'acide okadaïque (AO), la pecténotoxine-2 (PTX-2), la yessotoxine (YTX) et le spirolide (SPX-1), ont été sélectionnées. Le passage intestinal a été évalué à l’aide de cellules intestinales humaines Caco-2 mimant l’épithélium intestinal. Si des différences d’absorption ont été observées pour les 4 phycotoxines, nos résultats ont montré que l’épithélium intestinal était également capable de les renvoyer dans la lumière intestinale, limitant ainsi la quantité circulant dans l’organisme. De même, à l’aide d’extraits de foie, nous avons montré que la structure des 4 phycotoxines était modifiée, principalement par des réactions d'hydroxylation. Concernant les effets mélanges, l'ajout d'une autre toxine (PTX-2, YTX ou SPX-1) à l'AO entraîne des effets moins importants avec de faibles concentrations, et des effets additifs ou plus importants avec des concentrations plus élevées. Ces résultats apportent des données complémentaires pouvant servir à confirmer ou réviser les seuils réglementaires établis pour ces toxines
Lipophilic phycotoxins are secondary metabolites produced by some phytoplankton species. They accumulate in filter-feeding molluscs and can cause intoxication in humans with a wide variety of symptoms. This work aimed at bringing better knowledge on their fate in humans and their effects after ingestion by providing data on their intestinal absorption and their hepatic metabolism since these phenomena affect the amount of toxin circulating in the body and therefore the generation of toxic effects. In addition, several phycotoxins are sometimes found simultaneously in shellfish while the effects of these mixtures are still unknown. Four lipophilic phycotoxins, okadaic acid (OA), pectenotoxin-2 (PTX-2), yessotoxin (YTX) and spirolide (SPX-1) were selected. The intestinal passage was evaluated using human intestinal Caco-2 cells mimicking the intestinal epithelium. If differences in absorption were observed for the 4 phycotoxins, our results showed that the intestinal epithelium was also able to send them back into the intestinal lumen, thus limiting the amount circulating in the body. Similarly, using liver extracts, we showed that the structure of the 4 phycotoxins was modified, mainly by hydroxylation reactions. For mixtures effects, the addition of another toxin (PTX-2, YTX or SPX-1) to OA results in lower effects at low concentrations, and additive or larger effects at higher concentrations. These results provide additional data that can be used to confirm or revise regulatory thresholds established for these toxins

Social media has become an integral part of the Internet. There have been users across the world sharing content like images, texts, videos, and so on. There is a huge amount of data being generated and it has become a challenge to the social media platforms to group the content for further usage like recommending a video. Especially, grouping videos based on similarity requires extracting features. This thesis investigates potential approaches to extract features that can help in determining the similarity between videos. Features of given videos are extracted using Object Detection and Action Recognition. Bag-of-features representation is used to build the vocabulary of all the features and transform data that can be useful in clustering videos. Probabilistic model-based clustering, Multinomial Mixture model is used to determine the underlying clusters within the data by maximizing the expected log-likelihood and estimating the parameters of data as well as probabilities of clusters. Analysis of clusters is done to understand the genre based on dominant actions and objects. Bayesian Information Criterion(BIC) and Akaike Information Criterion(AIC) are used to determine the optimal number of clusters within the given videos. AIC/BIC scores achieved minimum scores at 32 clusters which are chosen to be the optimal number of clusters. The data is labeled with the genres and Logistic regression is performed to check the cluster performance on test data and has achieved 96% accuracy

Detecting human actions using a camera has many possible applications in the security industry. When a human performs an action, his/her body goes through a signature sequence of poses. To detect these pose changes and hence the activities performed, a pattern recogniser needs to be built into the video system. Due to the temporal nature of the patterns, Hidden Markov Models (HMM), used extensively in speech recognition, were investigated. Initially a gesture recognition system was built using novel features. These features were obtained by approximating the contour of the foreground object with a polygon and extracting the polygon's vertices. A Gaussian Mixture Model (GMM) was fit to the vertices obtained from a few frames and the parameters of the GMM itself were used as features for the HMM. A more practical activity detection system using a more sophisticated foreground segmentation algorithm immune to varying lighting conditions and permanent changes to the foreground was then built. The foreground segmentation algorithm models each of the pixel values using clusters and continually uses incoming pixels to update the cluster parameters. Cast shadows were identified and removed by assuming that shadow regions were less likely to produce strong edges in the image than real objects and that this likelihood further decreases after colour segmentation. Colour segmentation itself was performed by clustering together pixel values in the feature space using a gradient ascent algorithm called mean shift. More robust features in the form of mesh features were also obtained by dividing the bounding box of the binarised object into grid elements and calculating the ratio of foreground to background pixels in each of the grid elements. These features were vector quantized to reduce their dimensionality and the resulting symbols presented as features to the HMM to achieve a recognition rate of 62% for an event involving a person writing on a white board. The recognition rate increased to 80% for the "seen" person sequences, i.e. the sequences of the person used to train the models. With a fixed lighting position, the lack of a shadow removal subsystem improved the detection rate. This is because of the consistent profile of the shadows in both the training and testing sequences due to the fixed lighting positions. Even with a lower recognition rate, the shadow removal subsystem was considered an indispensable part of a practical, generic surveillance system.

Detecting human actions using a camera has many possible applications in the security industry. When a human performs an action, his/her body goes through a signature sequence of poses. To detect these pose changes and hence the activities performed, a pattern recogniser needs to be built into the video system. Due to the temporal nature of the patterns, Hidden Markov Models (HMM), used extensively in speech recognition, were investigated. Initially a gesture recognition system was built using novel features. These features were obtained by approximating the contour of the foreground object with a polygon and extracting the polygon's vertices. A Gaussian Mixture Model (GMM) was fit to the vertices obtained from a few frames and the parameters of the GMM itself were used as features for the HMM. A more practical activity detection system using a more sophisticated foreground segmentation algorithm immune to varying lighting conditions and permanent changes to the foreground was then built. The foreground segmentation algorithm models each of the pixel values using clusters and continually uses incoming pixels to update the cluster parameters. Cast shadows were identified and removed by assuming that shadow regions were less likely to produce strong edges in the image than real objects and that this likelihood further decreases after colour segmentation. Colour segmentation itself was performed by clustering together pixel values in the feature space using a gradient ascent algorithm called mean shift. More robust features in the form of mesh features were also obtained by dividing the bounding box of the binarised object into grid elements and calculating the ratio of foreground to background pixels in each of the grid elements. These features were vector quantized to reduce their dimensionality and the resulting symbols presented as features to the HMM to achieve a recognition rate of 62% for an event involving a person writing on a white board. The recognition rate increased to 80% for the "seen" person sequences, i.e. the sequences of the person used to train the models. With a fixed lighting position, the lack of a shadow removal subsystem improved the detection rate. This is because of the consistent profile of the shadows in both the training and testing sequences due to the fixed lighting positions. Even with a lower recognition rate, the shadow removal subsystem was considered an indispensable part of a practical, generic surveillance system.

Cette thèse porte sur l'étude de micro-plasmas froids à la pression atmosphérique générés à partir de différents réacteurs des configurations basées sur le principe des Décharges à Barrière Diélectrique (DBD) et alimentés par des générateurs de tension impulsionnelle et sinusoïdale. Les plasmas sont formés dans des gaz nobles tels que l'hélium et l'argon (gaz vecteurs), et également dans des mélanges réalisés avec des gaz moléculaires tels que l'azote et l'oxygène afin de produire des Espèces Réactives de l’Azote et de l’Oxygène (ERA, ERO). La (ré)activité chimique du plasma est ainsi supposée être accrue, permettant le traitement de matériaux inertes ou vivants pour diverses applications (fonctionnalisation de surfaces, inactivation de cellules, régénération de tissus vivants, etc.). La caractérisation des plasmas étudiés est réalisée en enregistrant les aspects électriques et optiques en fonction des paramètres élémentaires, comme l’amplitude et la fréquence de la tension, le débit du gaz, la configuration des électrodes, et le rapport cyclique dans le cas du régime pulsé. Ainsi, la (ré)activité chimique des plasmas est évaluée tandis que au même temps les mécanismes de la génération des plasmas et les façons de l’optimisation de la chimie sont dévoilées. Finalement, nous examinons l'efficacité du plasma dans le domaine biomédical en traitant divers systèmes biologiques (bactéries, liposomes, cellules) sans effets thermiques
The present PhD thesis is devoted to the study of atmospheric pressure cold micro-plasmas produced in different Dielectric Barrier Discharge (DBD) reactors which are driven by pulsed or sinusoidal high voltages. Noble gases such as helium and argon are used as carrier gases, whereas admixtures with nitrogen and oxygen are studied as well. The formation of Reactive Nitrogen and Oxygen Species (RNS, ROS) is thus achieved, and the possibility of improving the chemical (re)activity of the plasmas is demonstrated. This is of interest in the treatment of inert or living materials (e.g. surface functionalization, cell inactivation, living tissue regeneration, etc.). Plasmas are characterized by recording electrical and optical features as a function of principal operational parameters, including voltage amplitude and frequency, gas flow rate, electrode configuration, and voltage duty cycle in the case of pulsed waveform. The physico-chemical (re)activity of the plasmas is thus evaluated, while at the same time mechanisms on the plasma generation and paths for chemistry optimization are unveiled. Finally, the efficiency of the plasma in relation to biomedical applications is tested by treating different biological systems (bacteria, liposomes, cells) while preventing any thermal effect

High class mold is required for high quality castings. At present, the demands on molding materials are being extended by adding the strict requirement of environmentalists. A suitable variant that meets both demands are green sand molds. The goal of the thesis is to repeatedly cast experimental castings into molds made of 4 types of green sand mixtures. The technological properties of the molds will be compared, the degree of bentonite degradation will be assessed and the surface quality of castings will be assessed according to the amount of adherent molding mixture.

The present mini-thesis seeks to explore and investigate the mathematical theory and concepts that underpins the valuation of derivative securities, particularly European plainvanilla options. The main argument that we emphasise is that novel models of option pricing, as is suggested by Hull and White (1987) [1] and others, must account for the discrepancy observed on the implied volatility &ldquo
smile&rdquo
curve. To achieve this we also propose that market volatility be modeled as random or stochastic as opposed to certain standard option pricing models such as Black-Scholes, in which volatility is assumed to be constant.

Les sédiments de dragage constituent une ressources granulaire minérale alternative d’abondance et stratégique pour le domaine de la construction. Ce travail doctoral s’intéresse spécifiquement aux sédiments de dragage portuaire de Grand Port Maritime de Dunkerque (GPMD), issus de lagunage actif. L’objectif de la recherche est d’évaluer le potentiel de valorisation de ces sédiments sortant directement des bassins de lagunage du GPMD, (déshydratés en partie, mais faiblement humides) dans la formulation de bétons autoplaçants (BAP), sans aucun traitement additionnel avant leur incorporation dans les matériaux cimentaires (ni étuvage, ni calcination notamment).Trois sédiments GPMD ont été retenus pour l’étude, leur différence étant marquée par leurs teneurs en fines à 63 µm, respectivement de l’ordre de 34, 43 et 49%. Du fait de leur fort pourcentage en particules inférieures à 125 µm et de leur distribution granulométrique, l’intérêt de l’étude réside également dans l’évaluation de l’aptitude des sédiments à substituer les fillers minéraux naturels classiquement utilisés dans la composition de matrices cimentaires autoplaçantes.Un protocole expérimental spécifique est développé pour s’affranchir de la problématique de présence d’agglomérats de sédiments dans les matrices cimentaires.La méthodologie expérimentale globale de formulation s’articule autour de la méthode DMDA (Densified Mixture Design Algorithm) pour la composition des BAP, la méthode de l’AFREM et la méthode de la pâte équivalente. Sur l'ensemble des formulations réalisées, les performances physico-chimiques, rhéologiques, mécaniques, environnementales ainsi qu'une première approche de la durabilité vis-à-vis du gel-dégel sont étudiées. Les influences des fines de sédiments sur les performances mécaniques et la résistance au gel/dégel sont plus nuancées, les performances globales des matrices étant néanmoins avérées. D'un point de vue environnemental, les BAP développés sont classés comme matériaux inertes
Dredging sediments are an abundant and stand for a strategic alternative mineral granular resource in construction. This PhD work specifically focuses on the Grand Port Maritime de Dunkerque (GPMD) dredging sediments, resulting from an active lagooning. The research objective is to evaluate the potential for recovery of these sediments coming directly from the GPMD lagoon basins (partly dehydrated but poorly moist) in the formulation of self-consolidating concretes (SCC), without any additional treatment before their incorporation into the cementitious materials (without drying, nor calcination in particular).Three GPMD dredging sediments were selected for the study, their difference being their fines content at 63 μm, respectively of the order of 34, 43 and 49%. Because of their high percentage of particles smaller than 125 μm and their particle size distribution, the interest of the study also lies in the assessment of the ability of sediments to substitute the natural mineral fillers conventionally used in the composition of SCC.A specific experimental protocol is developed to overcome the problem of presence of sediment agglomerates in cementitious matrices. The overall experimental formulation methodology is based on the Densified Mixture Design Algorithm (DMDA) method for the determination of SCC compositions, the AFREM method and the equivalent paste method. On the set of formulations carried out, the physical-chemical, rheological, mechanical and environmental performances as well as a first approch of the durability with regard to freeze-thaw are studies. The influences of sediment fines on mechanical performance and freeze / thaw resistance are more nuanced, although the overall performance of the matrices is proven. From an environmental point of view, the developed SCCs are classified as inert materials

The project consists of two distinct levels i.e. separation level and diagnostic level. At the separation level, statistical models of gaussians and color are separately used to classify each pixel as belonging to backgroung or foreground. Adopted method is mixture of gaussians.A mixture of gaussians model is suitable here because the results of the picture tests will not depend on the lens opening, but rather on the colors in the backgroung. A mixture of gaussians model for return data seems reasonable. The achieved results the used method on the real sequences are presented in the thesis. Diagnostic level is identified human body on the scene. Adopted method is ASM(Active Shape Models) with PCA(Principal Component Analysis). ASM are statistical models of the shape of human bodies which iteratively deform to fit to an example of the object in a new image.

La population générale est exposée à un grand nombre de pesticides, principalement via son alimentation. Alors que ces matières actives ont reçu une autorisation de mise sur le marché individuelle, l’effet sur l’organisme humain d’un mélange de tels composés est en revanche très peu connu. Afin de contribuer à mieux appréhender cet « effet mélange », notre étude s’est attachée à étudier le métabolisme hépatique humain in vitro de deux mélanges de pesticides communément retrouvés dans l’alimentation française
General population is exposed to several pesticides, mainly via the diet. Whereas these active ingredients obtained their marketing authorization individually, the available data regarding their impact as a mixture on the human body are scarce. In order to help better understanding this “mixture effect”, we aimed at studying the human hepatic in vitro metabolism of two pesticides mixtures commonly found in the diet

Розроблене навісне ударно-вібраційне обладнання з гідравлічним приводом від базової гідрофікованої вантажопідйомної машини. Проведені випробування, які підтвердили придатність і практичну доцільність цього устаткування до застосування у будівельній галузі. Наведені рекомендації щодо проектування та технології застосування цього устаткування у виробничих умовах.
Designed mounted shock vibration equipment with hydraulic drive hydroficated from the base of the machine. Tests have been carried out, which confirmed the suitability and practical expediency of this equipment for use in the construction industry. The recommendations for the design and technology of the use of this equipment in the production conditions are given.

Purpose: The main objective of this research project is to address the limitations of image-processing computational performance of current ultrasound target motion estimation techniques by developing a novel high-performance ultrasound motion estimation technique that eliminates the need for using currently adopted image-registration-based motion-estimation techniques for systems requiring ultrasound target tracking. To address the system's dependence on the operator's experience and supervision as the second objective of this research project, the developed target tracking technique is integrated with a novel automation platform developed to support medical physicists with tools for collectively implementing, supervising, and training arbitrary ultrasound target motion estimation tasks and incorporate them in the platform as reusable solutions to support qualified and reproducible research. Methodologies: The main objective of this research project has been addressed by enabling high-performance and accurate motion estimation of soft-tissue-equivalent ultrasound targets using the ultrasound direct visual servoing (US-DVS) technique for the first time. The inaccurate US-target tracking capabilities of the implemented US-DVS technique have been addressed and optimised using specially trained machine-learning models which lead to the US direct visual modelling (US-DVM) technique introduced by this project. The machine-learning models implemented by the US-DVM technique were trained using two types of US-target motion simulations: simulation of tissue-equivalent US-target motion based on predefined motion trajectories provided by high-precision robotic-arms; and simulations using an ultrasound digital-target dynamics simulator (US-DTDS) developed by this project. The second objective of this research project has been addressed by maximising the performance and target detection accuracy of the proposed motion estimation technique by minimising its dependence on the operator and by transferring the operator's target scanning and identification experience to a provenance-enabled automation system. To Achieve this, another machine-learning model, based on Gaussian mixture modelling (GMM), was also developed and used to improve the performance of standard image segmentation techniques allowing for automating target detection and tracking in real-time. In addition, the interaction of the operator with the platform has been optimised by employing a provenance-enabled workflow automation framework, called VisTrails, to implement the proposed new technique and all the supporting services required. This will help in learning the operator's skills by the automation workflow, which will minimise the operators' systematic errors and support reproducible research. Results: A Medical Physics Services Framework (MPS-F) has been developed based on VisTrails and used to control two robotic arms to track and capture the simulated motion using the US-DVM technique. The new US-DVM technique has enabled accurate estimation of ultrasound target motion from US-DVS tracking feedback with accuracies better than 1.5%, and with computational performance up to 14 times better than motion estimation techniques used in current practice. This allows for more accurate real-time tracking of ultrasound targets like the prostate. Regarding the second objective, high-performance detection and extraction of deformable ultrasound targets using the morphological active-contour technique (MACT) has been achieved for average prostate-size targets to within 0.04 seconds using down-sampling strategies. To further support the second objective, the MPS-F has been developed as a provenance-enabled software automation solution to enable other researchers to reuse and reproduce most of the implementations and results of this research, and hence minimise the operator's systematic errors. The MPS-F has been used to implement a novel technique that combined the MACT and the US-DVM to detect and estimate prostate-size target deformations with volume accuracies better than 0.005 cm^3. Conclusion: This research study introduced the US-DVM technique as a novel ultrasound target motion modelling and estimation solution based on ultrasound direct visual servoing (US-DVS). US-DVS is used typically for ultrasound target tracking in real-time and using it for modelling and estimating target dynamics has been addressed for the first time by this study based on machine learning strategies. The machine learning approach provided solutions that overcame inherent limitations of the imaging system allowing for predicting faster dynamics and larger interframe displacements, in addition to enabling supervised and automated predictions of accurate motion estimations tailored specifically for individual targets for optimal consistency and accuracy. The proposed techniques and solutions have been implemented and evaluated by the medical physics services framework (MPS-F), which was developed by this project based on the VisTrails workflow management system. The MPS-F is considered a major contribution by this study where it enables the operator to implement, train, and supervise arbitrary medical physics workflows that can employ machine-learning, image-processing, and ultrasound target tracking and motion estimation tasks. With the help of the MPF-S, it is proposed by this study that an ultrasound modelling and automation platform (US-MAP) can be constructed as a more efficient real-time alternative for the Elekta Clarity Autoscan system being the only non-telerobotic real-time ultrasound target tracking system implemented clinically for tracking prostate motion.

To answer the question who spoke when, speaker diarization (SD) is a critical step for many speech applications in practice. The task of our project is building a MFCC-vector based speaker diarization system on top of a speaker verification system (SV), which is an existing Call-centers application to check the customer’s identity from a phone call. Our speaker diarization system uses 13-Dimensional MFCCs as Features, performs Voice Active Detection (VAD), segmentation, Linear Clustering and the Hierarchical Clustering based on GMM and the BIC score. By applying it, we decrease the Equal Error Rate (EER) of the SV from 18.1% in the baseline experiment to 3.26% on the general call-center conversations. To better analyze and evaluate the system, we also simulated a set of call-center data based on the public audio databases ICSI corpus.
För att svara på frågan vem som talade när är högtalardarisering (SD) ett kritiskt steg för många talapplikationer i praktiken. Uppdraget med vårt projekt är att bygga ett MFCC-vektorbaserat högtalar-diariseringssystem ovanpå ett högtalarverifieringssystem (SV), som är ett befintligt Call-center-program för att kontrollera kundens identitet från ett telefonsamtal. Vårt högtalarsystem använder 13-dimensionella MFCC: er som funktioner, utför Voice Active Detection (VAD), segmentering, linjär gruppering och hierarkisk gruppering baserat på GMM och BIC-poäng. Genom att tillämpa den minskar vi EER (Equal Error Rate) från 18,1 % i baslinjeexperimentet till 3,26 % för de allmänna samtalscentret. För att bättre analysera och utvärdera systemet simulerade vi också en uppsättning callcenter-data baserat på de offentliga ljuddatabaserna ICSI corpus.

Pharmaka werden nach ihrer Einnahme bzw. Verabreichung über verschiedene Pfade in die Umwelt eingetragen. Obwohl Arzneimittel zu den toxikologisch best-untersuchten und -charakterisierten Stoffen gehören, ist ihre Wirkung auf die Umwelt und die darin lebenden Organismen weit weniger gut untersucht. Wenn in der Literatur Daten zur Ökotoxizität vorhanden sind, so beziehen sich diese meist nur auf die Wirkung von Einzelstoffen. In der Umwelt sind die Organismen jedoch gegenüber Mischungen exponiert. Aufgrund der geschilderten Problematik wurden eine Reihe von Arzneimitteln unterschiedlicher Indikationsgruppen einzeln und in Kombination mit dem Embryotest mit dem Zebrabärbling (Danio rerio, DarT) untersucht. Dieses Testsystem wurde durch Schulte & Nagel (1994) als Alternativmethode zum akuten Fischtest nach OECD 203 entwickelt und bietet den Vorteil neben letalen auch eine Reihe von subletalen Endpunkten erfassen zu können. Es handelt sich zudem nach dem deutschen Tierschutzgesetz nicht um einen Tierversuch. Die generelle Vergleichbarkeit der ermittelten Werte mit Daten aus akuten Fischtests nach OECD 203 sowie die Anwendbarkeit für verschiedenste Fragestellungen konnten in einer Reihe von Studien gezeigt werden (Nagel, 2002). Für die hier vorgestellten Untersuchungen wurden zunächst 32 Pharmaka und drei Pflanzenschutzmittel als Einzelstoffe mit dem DarT untersucht. Basierend auf den Ergebnissen der Einzelstofftests wurden Mischungen sowohl aus Substanzen mit ähnlichen als auch unähnlichen Wirkmechanismen getestet. Es zeigte sich, dass unabhängig vom Wirkmechanismus die Mischungstoxizität durch das Konzept der Konzentrationsadditivität gut vorhergesagt wurde, während das Konzept der Unabhängigen Wirkung die Mischungstoxizität unterschätzte. Ebenfalls konnte gezeigt werden, dass die Kombination der Stoffe auf Basis der NOEC, die im DarT anhand der Herzschlagfrequenz nach 48 Stunden ermittelt wird, zu deutlichen Mischungseffekten führt.

La transition d'une agriculture diversifiée à un système productiviste a entraîné une perte de diversité cultivée et pose de nombreux enjeux environnementaux, sociétaux et de santé. Des alternatives telles que l'agro-écologie ont émergé, reposant sur la valorisation de l'agro-biodiversité, notamment de la diversité génétique au sein des agroécosystèmes. Constatant qu'aucune des variétés du catalogue n'est adaptée à leurs besoins, des paysan.ne.s et animateur.trice.s du Réseau Semences Paysannes (RSP) mènent depuis 2006, en collaboration avec l'équipe DEAP (Diversité, Évolution et Adaptation des Populations) de l'UMR GQE Le Moulon, un projet de sélection participative (SP) du blé tendre. Ces paysan.ne.s mobilisent la diversité pour sélectionner des populations adaptées à leurs pratiques, terroirs et débouchés, dans le but de retrouver une autonomie semencière et une cohérence de leur système. Ma thèse porte sur l'étude des impacts des pratiques de gestion collective et de sélection paysanne sur la diversité cultivée du blé et l'adaptation des populations. Elle vise à proposer des adaptations éventuelles des pratiques de SP existantes et d'appuyer la mise en place de nouveaux projets. Les impacts de pratiques de création et sélection à la ferme de mélanges de populations sur leur comportement agronomique et morphologique ont été évalués par une expérimentation en collaboration avec une quinzaine de paysan.ne.s et animateur.trice.s du RSP. Dans une deuxième partie nous avons étudié les impacts de la sélection naturelle et la sélection paysanne sur l'évolution des populations, leur stabilité et leur adaptation aux environnements au cours du projet de SP blé. Ensuite une étude prospective a porté sur les impacts de l'adoption de peuplements hétérogènes sur la diversité cultivée à l'échelle du paysage, par l'évaluation de la diversité des populations issues de SP, la simulation de scénarii d'adoption des peuplements hétérogènes et l'utilisation d'indicateurs de la diversité cultivée. Enfin, je me suis intéressée aux impacts qu'ont les paramètres du dispositif expérimental mis en place sur les fermes sur l'ajustement et la précision des estimations par les modèles Bayésiens utilisés, afin d'améliorer notre capacité à détecter des différences significatives entre populations et de donner des recommandations pour d'autres projets d'évaluation décentralisée de variétés utilisant les dispositifs et modèles développés dans projet SP blé français
The transition from a diversified agriculture to a productivist system has led to a decline in cultivated diversity and raises many environmental, societal and health issues. Alternatives such as agro-ecology have emerged, based in particular on the enhancement of agro-biodiversity and genetic diversity within agro-ecosystems. Considering that there are no varieties adapted to their needs in the catalogue, farmers and facilitators from the Réseau Semences Paysannes (RSP) have been conducting a participatory breeding project (PPB) for bread wheat since 2006, in collaboration with the DEAP (Diversity, Evolution and Adaptation of Populations) team at UMR GQE Le Moulon. These farmers are mobilizing diversity to select populations adapted to their practices, terroir and outlets, with the aim of regaining their seed autonomy and a coherence of their system. My thesis focuses on the study of the impacts of collective management and peasant selection practices on wheat crop diversity and population adaptation. It aims to propose possible adaptation of existing PPB practices and to support the implementation of new projects. The impacts of on-farm creation and selection practices of population mixtures on their agronomic and morphological behaviour were evaluated through an experiment in collaboration with about fifteen farmers and facilitators from the RSP. In a second part we studied the impacts of natural selection and peasant selection on the evolution of populations, their stability and adaptation to environments during the wheat PPB project. Then a prospective study on the impacts of the adoption of heterogeneous varieties on cultivated diversity at the landscape level was conducted, by assessing the diversity of populations from PPB, simulating adoption of heterogeneous varieties scenarii and using cultivated diversity indicators. Finally, the impacts of the on-farm experimental design parameters on the adjustment and accuracy of estimates from Bayesian models were assessed, to improve our ability to detect significant differences between populations and to provide recommendations for other decentralized variety evaluation projects using the designs and models developed in the French wheat PPB project

Doutoramento em Biologia
During the last century mean global temperatures have been increasing. According to the predictions, the temperature change is expected to exceed 1.5ºC in this century and the warming is likely to continue. Freshwater ecosystems are among the most sensitive mainly due to changes in the hydrologic cycle and consequently changes in several physico-chemical parameters (e.g. pH, dissolved oxygen). Alterations in environmental parameters of freshwater systems are likely to affect distribution, morphology, physiology and richness of a wide range of species leading to important changes in ecosystem biodiversity and function. Moreover, they can also work as co-stressors in environments where organisms have already to cope with chemical contamination (such as pesticides), increasing the environmental risk due to potential interactions. Therefore, the objective of this work was to evaluate the effects of climate change related environmental parameters on the toxicity of pesticides to zebrafish embryos. The following environmental factors were studied: pH (3.0-12.0), dissolved oxygen level (0-8 mg/L) and UV radiation (0-500 mW/m2). The pesticides studied were the carbamate insecticide carbaryl and the benzimidazole fungicide carbendazim. Stressors were firstly tested separately in order to derive concentration- or intensity-response curves to further study the effects of binary combinations (environmental factors x pesticides) by applying mixture models. Characterization of zebrafish embryos response to environmental stress revealed that pH effects were fully established after 24 h of exposure and survival was only affected at pH values below 5 and above 10. Low oxygen levels also affected embryos development at concentrations below 4 mg/L (delay, heart rate decrease and edema), and at concentrations below 0.5 mg/L the survival was drastically reduced. Continuous exposure to UV radiation showed a strong time-dependent impact on embryos survival leading to 100% of mortality after 72 hours of exposure. The toxicity of pesticides carbaryl and carbendazim was characterized at several levels of biological organization including developmental, biochemical and behavioural allowing a mechanistic understanding of the effects and highlighting the usefulness of behavioural responses (locomotion) as a sensitive endpoint in ecotoxicology. Once the individual concentration response relationship of each stressor was established, a combined toxicity study was conducted to evaluate the effects of pH on the toxicity of carbaryl. We have shown that pH can modify the toxicity of the pesticide carbaryl. The conceptual model concentration addition allowed a precise prediction of the toxicity of the jointeffects of acid pH and carbaryl. Nevertheless, for alkaline condition both concepts failed in predicting the effects. Deviations to the model were however easy to explain as high pH values favour the hydrolysis of carbaryl with the consequent formation of the more toxic degradation product 1- naphtol. Although in the present study such explanatory process was easy to establish, for many other combinations the “interactive” nature is not so evident. In the context of the climate change few scenarios predict such increase in the pH of aquatic systems, however this was a first approach focused in the lethal effects only. In a second tier assessment effects at sublethal level would be sought and it is expectable that more subtle pH changes (more realistic in terms of climate changes scenarios) may have an effect at physiological and biochemical levels with possible long term consequences for the population fitness.
Durante o século passado, as temperaturas globais médias têm vindo a aumentar. De acordo com as previsões, a mudança de temperatura deverá ser superior a 1,5ºC neste século e o aquecimento é provável que continue. Os ecossistemas de água doce estão entre os mais sensíveis, principalmente devido às mudanças no ciclo hidrológico e, consequentemente, em diversos parâmetros físico-químicos (ex. pH, oxigénio dissolvido). Alterações nos parâmetros abióticos de ambientes de água doce irão provavelmente afectar a distribuição, morfologia, fisiologia e riqueza de uma ampla gama de espécies levando a mudanças importantes na biodiversidade e funcionamento do ecossistema. Para além disto, eles também podem atuar como co-estressores em ambientes onde os organismos já tem que lidar com contaminação química. Portanto, o objetivo deste trabalho foi avaliar os efeitos de parâmetros ambientais sobre a toxicidade dos pesticidas para embriões de peixe-zebra. Foram estudados os seguintes fatores ambientais: pH (3,0-12,0), nível de oxigénio dissolvido (0-8 mg/L) e radiação UV (0-500 mW/m2). Os pesticidas estudados foram o inseticida carbamato carbaril e o fungicida benzimidazólico carbendazim. Ambos os estressores (fatores ambientais e pesticidas) foram testados separadamente a fim de obter curvas dose-resposta para estudar mais profundamente os efeitos combinados de estressores ambientais e toxicidade química, aplicando modelos de mistura. A caracterização das respostas do peixe-zebra ao estresse ambiental mostrou que os efeitos do pH foram totalmente estabelecidas após 24 h de exposição e a sobrevivência foi só afetada a valores de pH abaixo de 5 e acima 10. Os níveis reduzidos de oxigénio também afetaram o desenvolvimento dos embriões em concentrações abaixo de 4 mg/L (atraso, redução dos batimentos cardíacos e edema) e em concentrações abaixo de 0.5 mg/L a sobrevivência foi drasticamente reduzida. A exposição contínua a radiações UV mostrou um forte efeito dependente do tempo na sobrevivência dos embriões levando a 100% de mortalidade no final do ensaio. A toxicidade dos pesticidas carbaril e carbendazim foi caracterizada em vários níveis de organização biológica, incluindo desenvolvimento, biomarcadores e comportamental, permitindo uma compreensão mecanicista dos efeitos e destacando a utilidade de respostas comportamentais (locomoção) como um parâmetro sensível em ecotoxicologia. Uma vez que as curvas dose resposta para cada estressor foram estabelecidas, um estudo de toxicidade combinado foi realizado para avaliar os efeitos do pH sobre a toxicidade do carbaril. Os resultados mostraram que o pH pode modificar a toxicidade do pesticida carbaryl. O modelo conceitual de adição da concentração permitiu uma previsão precisa da toxicidade dos efeitos conjuntos do pH ácido e carbaril. No entanto, para a condição alcalina ambos os conceitos falharam na previsão dos efeitos. Os desvios ao modelo foram no entanto fáceis de explicar uma vez que os valores de pH elevados favoreceram a hidrólise do carbaril com a consequente formação de um produto de degradação mais tóxico 1-naftol. Embora no presente estudo tal processo explicativo foi fácil de estabelecer, para muitas outras combinações de natureza "interativa" talvez esse processo não seja tão evidente. No contexto das alterações climáticas poucos cenários preveem um aumento tão elevado do pH de sistemas aquáticos, no entanto, esta pode ser considerada uma primeira abordagem focada apenas nos efeitos letais. Numa segunda avaliação, efeitos ao nível sub-letal seriam recomendados uma vez que espera-se que mudanças mais sutis de pH (mais realistas em termos de cenários de mudanças climáticas) possam ter um efeito em níveis fisiológicos e bioquímicos, com possíveis consequências a longo prazo para o fitness das populações.

Les données scientifiques actuelles suggèrent un déclin de la diversité et de l’abondance des insectes, y compris les abeilles domestiques Apis mellifera. Ces dernières sont confrontées à de fortes pertes de colonies dans plusieurs régions du monde telles que l’ouest de l’Europe et les États-Unis. De nombreuses études suggèrent que l’origine du déclin des colonies d’abeilles est multicausale et identifient les pesticides et les agents pathogènes comme étant les principaux contributeurs à ce déclin. La co-exposition des abeilles à de multiples pesticides et l’infection par plusieurs pathogènes constituent un phénomène courant. Cependant, les recherches sur les effets des mélanges de pesticides n’ont pas fait l’objet d’un intense développement. Ainsi, les travaux conduits dans le cadre de cette thèse ont été focalisés sur la détermination de la toxicité des mélanges de pesticides, appliqués à des niveaux d’exposition environnementaux, en présence d’un agent pathogène. Le choix s’est porté sur l’étude des interactions entre un insecticide néonicotinoïde, l’imidaclopride, un fongicide azole, le difénoconazole, et un herbicide, le glyphosate, en présence de l’agent pathogène Nosema ceranae. Les résultats des différentes études effectuées durant cette thèse, révèlent la complexité des études sur les mélanges de pesticides. Ces travaux nous ont permis de constater que les effets d’un mélange de pesticides peuvent fortement varier en fonction des concentrations des pesticides constituant le mélange. L’augmentation du nombre de substances et du niveau d’exposition, n’induit pas nécessairement une augmentation de la toxicité du mélange. De plus, les effets du mélange peuvent varier en fonction de la séquence d’exposition aux pesticides et de l’état sanitaire des abeilles. Les mélanges de pesticides affectent l’état physiologique des abeilles suite à une réponse systémique liée à des perturbations de mécanisme généraux tels que le stress oxydant. Cependant, ces trois pesticides, seuls et en mélanges n’ont aucun effet sur l’installation du microbiote intestinal à des niveaux d’exposition environnementaux
Current scientific findings suggest a decline in the diversity and abundance of insects, including the honey bee Apis mellifera. The latter are facing high colony losses in several regions of the world such as Western Europe and the United States. Numerous studies suggest that the origin of bee colony decline is multi-causal and identify pesticides and pathogens as the main contributors to this decline. Co-exposure of honey bees to multiple pesticides and infection by multiple pathogens are common phenomena. However, research on the effects of pesticide mixtures has not been extensively developed. Thus, the thesis work has focused on determining the toxicity of pesticide mixtures, applied at environmental exposure levels, in the presence of pathogens. The choice was made to study the interactions between a neonicotinoid insecticide, imidacloprid, an azole fungicide, difenoconazole, and a herbicide, glyphosate, in the presence of the pathogen Nosema ceranae. The results of the different studies, carried out during this thesis, reveal the complexity of the studies on pesticide mixtures. The work allowed us to notice that the effects of a pesticide mixture can vary according to the concentrations of the pesticides constituting the mixture. The increase of the number of substances and the level of exposure does not necessarily induce an increase of the toxicity of the mixture. Furthermore, the effects of the mixture may vary depending on the sequence of exposure to the different pesticides and the health status of the honey bees. Pesticide mixtures affect the physiological state of individuals as a result of a systemic response related to disturbances of general mechanisms such as oxidative stress. However, these three pesticides, alone and in mixtures, have no effect on the installation of the intestinal microbiota at environmental exposure levels

Perseguendo la ricerca di una nuova classe di peptidi antimicrobici strutturalmente semplici, abbiamo ottimizzato una sintesi breve, economica e ad alto rendimento di derivati dell'acido α-idrazido anfifilico monocarico, con azione membranolitica. Tali composti, hanno esibito un'attività in vitro ad ampio spettro contro una varietà di batteri Gram-positivi e Gram-negativi, tra cui due ceppi multi-farmaco resistenti. Inoltre, hanno mostrato effetti sinergici con la tetraciclina nei confronti dei batteri sensibili, mentre sono stati osservati effetti sinergici o indifferenza per combinazioni con diversi antibiotici di prima linea verso ceppi multiresistenti. Nonostante la minima carica cationica, i migliori composti hanno dimostrato di essere selettivi verso le membrane cellulari batteriche rispetto alle membrane cellulari dei mammiferi. È stata anche dimostrata l'importanza di un'anfifilicità senza interruzioni. Con l'obiettivo di somministrare dosi più basse di colistina riducendo gli effetti collaterali tossici, il Dipartimento di biologia chimica dell'HZI (Braunschweig, Germania) ha sviluppato un nuovo costrutto peptide-colistina. Consiste in una miscela di cinque regioisomeri in cui ciascuno dei gruppi amminici liberi della colistina è legato al terminale C con un peptide sintetico. La scissione del gruppo ammide introdotto da parte dei neutrofili dell'elastasi umana, rilascia la colistina direttamente sulla superficie dei batteri per ucciderli. Pertanto, sfruttando la metodologia della fase solida, abbiamo preparato in modo regioselettivo gli isomeri del costrutto della colistina al fine di indagare se tutti i regioisomeri subiscono la scissione selettiva da parte dell’ elastasi con la stessa efficacia e fedeltà. Quindi, abbiamo eseguito i test antimicrobici contro un ceppo di E. coli K12 e i risultati sono stati confrontati con l'attività della miscela regioisomerica.
Pursuing the search for a new class of structurally simple mimics of antimicrobial peptides, we have optimized a short, cheap and high-yielding synthesis of mono-charged amphiphilic α-hydrazido acid derivatives, having a membranolytic action. They exhibited a broad-spectrum in vitro activity against a variety of Gram-positive and Gram-negative bacteria, including two multidrug-resistant strains. In addition, they showed synergistic effects with tetracycline toward sensitive bacteria, whereas either synergistic effects or indifference were observed for combinations with different first-line antibiotics toward multidrug-resistant strains. Despite the minimal cationic charge, the best compounds demonstrated to be selective toward bacterial cell membranes over mammalian cell membranes. The importance of a non-disrupted amphiphilicity was also demonstrated. With the aim to administer lower doses of colistin reducing the toxic side effects, the Department of Chemical Biology at HZI (Braunschweig, Germany) developed a novel peptide-colistin construct. It consists of a mixture of five regioisomers where each of its free amino groups of colistin was coupled to the C-terminal of a synthetic peptide. The cleavage of the newly introduced amide group by human elastase neutrophils, releases colistin directly on the surface of bacteria in order to kill them. Thus, exploiting solid phase methodology, we regioselectively prepared the isomers of the colistin construct in order to investigate if all the regioisomers undergo selective cleavage by elastase with the same efficacy and fidelity. Then, we carried out the antimicrobial assays against a strain of E. coli K12, and the results were compared with the activity of regioisomeric mixture.

Tese de mestrado, Engenharia Farmacêutica, Universidade de Lisboa, Faculdade de Farmácia, 2014
O primeiro objectivo desta tese foi o desenvolvimento de um método de quantificação por espectroscopia de infravermelho próximo de modo a optimizar um processo de fabrico da OM Pharma numa fase crítica de produção: fase final da mistura. Em seguida avaliou-se a aplicabilidade do mesmo tipo de estratégia ao controlo (identificação, qualificação e quantificação) de outros pontos críticos do processo. A necessidade da implementação desta metodologia incide no facto de a este processo estar associado um volume de trabalho significativo de trabalho do Controlo de Qualidade. O modelo de quantificação desenvolvido permite a determinação do parâmetro de qualidade crítico do processo de fabrico do produto: a conformidade do teor em API na mistura; após a verificação da conformidade processo produtivo evolui para outra fase – produto final. A aplicação desta técnica desenvolvida permite, em rotina, a redução do tempo despendido em análise pelo Controlo de Qualidade. O modelo obtido foi validado de acordo com as Guidelines em vigor. Um segundo objectivo, foi o de generalizar a aprendizagem anterior e desenvolver uma biblioteca para diversas matérias-primas (princípios activos farmacêuticos) que permitisse a sua identificação e no futuro possivelmente a sua qualificação; esta necessidade surge devido à elevada quantidade de lotes de matériaprima recepcionada periodicamente na OM Pharma. A criação da biblioteca consiste no desenvolvimento de um método que permita identificar o princípio activo referido no modelo de quantificação, o que acarreta a construção de uma Biblioteca de Princípios Activos (API) obtida pela aquisição de espectros NIR de todos os API´s da OM Pharma. A biblioteca desenvolvida foi sujeita a validação interna e externa de acordo com os requisitos das Guidelines em vigor. Concluiu-se que a espectroscopia de infravermelho próximo é um método preciso e benéfico para a análise e controlo de qualidade no controlo da fase final de produção e na identificação de matérias-primas na Indústria Farmacêutica. Associada à utilização desta técnica, o aumento da produtividade através da redução do tempo de análise e, consequentemente, a redução dos custos operativos é sem dúvida um factor muito positivo.
The first goal of this thesis was the development of a near infrared quantification method in order to optimize the mixing process in OM Pharma’s production phase, followed by the application of this method in controlling other critical processes such as identification, qualification and quantification. The fact that this process is associated with a significant part in Quality Control’s work volume justified the implementation of this methodology. The developed quantification PLS model allows the determination of a product manufacturing process critical quality parameter: the compliance of the API content; after checking this production phase conformity, the process evolves into another phase - final product. The application of this technique allows the reduction of the spent time on routine analysis. The model was validated according to the guidelines. A second goal consisted in developing a library allowing to identify several raw materials (pharmaceutical active ingredients) and in the future it’s possible qualification. This need arose due to the high amount of raw material batches periodically received in OM Pharma. The library development is based on a method developed for identification of the active principle in said quantization model which leads to the construction of a library of active ingredients (API) obtained by the acquisition of NIR spectrum. The developed library was subjected to internal and external validation according to the requirements of the Guidelines in effect. The near infrared spectroscopy method proved itself as an accurate and beneficial method for the analysis and quality control in controlling the final stages of production and raw materials identification in the pharmaceutical industry. Associated to the use of this technique, increased productivity by reducing the analysis time and, consequently, the reduction of operating costs is without a doubt very positive.

For many types of learners one can compute the statistically 'optimal' way to select data. We review how these techniques have been used with feedforward neural networks. We then show how the same principles may be used to select data for two alternative, statistically-based learning architectures: mixtures of Gaussians and locally weighted regression. While the techniques for neural networks are expensive and approximate, the techniques for mixtures of Gaussians and locally weighted regression are both efficient and accurate.

The thesis entitled “Novel Redox Responsive Cationic Lipids, Lipopolymers, Glycolipids and Phospholipid-Cationic Lipid Mixtures: Syntheses, Aggregation and Gene Transfection Properties” elucidates the design, synthesis, aggregation and gene transfection properties of novel cholesterol based cationic lipids with ferrocene as the redox moiety, polyethylenimine based ferrocenylated lipopolymers and cholesterol based non-ionic glycolipids. The thesis also discusses the cationic phospholipid-cationic lipid mixtures as superior gene transfection agents. The work has been divided into six chapters. Chapter 1. Introduction Part A. Various Cholesterol based Systems for Applications as Biomaterials Liposomes composed of cationic lipids have become popular gene delivery vehicles. A great deal of research is being pursued to make efficient vectors by varying their molecular architecture. Cholesterol being ubiquitous component in most of the animal cell membranes is increasingly being used as a hydrophobic segment of synthetic cationic lipids. In this chapter we describe various cholesterol based cationic lipids and focus on the effect of modifying various structural segments like linker and the headgroup of the cationic lipids on gene transfection efficiency with a special emphasis on the importance of ether linkage between cholesteryl backbone and the polar headgroup. Interaction of cationic cholesteryl lipids with dipalmitylphosphatidycholine membranes is also discussed here. Apart from cholesterol being an attractive scaffold in the drug/gene delivery vehicles, certain cholesteryl derivatives have also been shown to be attractive room temperature liquid-crystalline materials. Part B. Diverse Applications of Ferrocene Derivatives This chapter gives a brief overview of ferrocene chemistry followed by description of major applications of ferrocenyl derivatives in a variety of fields like catalysis, materials chemistry, electrochemical sensors, medicinal chemistry etc. We discuss the use of ferrocene as an electrochemical and redox active switch to achieve control over supramolecular aggregation. It also reviews ferrocene based amphiphiles including surfactants, lipids and polymers with an emphasis on the role of ferrocene over aggregate formation and their utilization in biological applications. Chapter 2: Optimization of Redox Active Alkyl-Ferrocene Modified Polyethylenimines for Efficacious Gene Delivery in Serum 1a-c, n = 6, P8-C6-F1, P8-C6-F2, P8-C6-F3 2a-c, n = 11, P8-C11-F1 P8-C11-F2, P8-C11-F3 % ferrocene grafting, F1 = 15%, F2 = 25% and F3 = 50% Figure 1. Structure of the alkyl-ferrocene modified 800 Da Branched Polyethylenimine. In this chapter we present six new lipopolymers based on low molecular weight polyethylenimines (BPEI 800 Da) which are hydrophobically modified using ferrocene terminated alkyl tails of variable lengths. The effects of degree of grafting, spacer length and redox state of ferrocene in the lipopolymer on the self assembly properties were investigated in detail by transmission electron microscopy (TEM), atomic force microscopy (AFM), dynamic light scattering (DLS) and zeta potential measurements. The assemblies displayed a redox induced increase in the size of the aggregates. The coliposomes comprising of the lipopolymer and a helper lipid 1,2-Dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE) showed excellent gene delivery capability in serum containing environment in two cancer cell lines (HeLa, U251 cells). Optimized formulations showed remarkably higher transfection activity than BPEI 25 KDa and even better than commercial Lipofectamine 2000 as evidenced from luciferase activity and EGFP expression analysis. Oxidation of ferrocene in lipopolymers led to reduced levels of gene transfection which was also followed by cellular internalization of fluorescently labeled pDNA using confocal microscopy. Cytotoxicity assay revealed no obvious toxicity for the lipopolyplexes in the range of optimized transfection levels. Overall, we have exploited the redox activity of ferrocene in PEI based polymeric gene carriers for trenchant control over gene transfection potential. RLU/mg protein HeLa Cells Figure 2. Maximum transfection efficacies of optimized redox lipopolymer/DOPE formulations by (A) Luciferase Assay and (B) Flow cytometry (GFP expression). Chapter 3. Membranes derived from Redox-active Cholesterol based Cationic Lipids and their Interactions with DNA and Phospholipid Membranes Figure 3. Molecular structures of the electroactive cholesterol based monomeric and gemini lipids. This chapter describes the synthesis and aggregation properties of two series of redox-active ferrocene containing monomeric and gemini cationic lipids with cholesterol as a hydrophobic domain. These cationic lipids are modified at their headgroup region using ferrocene terminated alkyl chains of differing length. All the four cationic lipids formed stable suspensions in water. Aggregation behavior of these cationic lipids in aqueous suspensions in their unoxidized and oxidized state was studied using TEM, DLS, zeta potential measurements and XRD studies. Cationic lipids with ferrocene in natural, reduced state were found form bigger sized vesicles which upon oxidation became smaller aggregates with increased zeta potential. XRD results indicate the existence of nice lamellar arrangements of the lipid bilayers. Thermotropic phase transition behavior of DPPC membranes incorporated with cationic ferrocene lipids was also studied using differential scanning calorimetry. Finally, we assayed pDNA (plasmid DNA) binding ability of all the four cationic lipids using ethidium bromide intercalation assay where all the cationic lipid formulations showed excellent DNA binding capability. In the experiments involving SDS-induced release of DNA, we observed that redox-active monomeric lipids (3a-b) were found to be more efficient in facilitating the release of DNA from the liposome-DNA complex in the presence of negatively charged SDS micelles than their gemini counterparts (4a-b). Chapter 4. Redox-responsive Gene Delivery by Ferrocene containing Cationic Cholesteryl Lipids in Serum This chapter describes the transfection efficacy of redox-active monomeric and gemini cationic lipids with cholesterol backbone. The transfection efficiency of all the lipids could be tuned by changing the oxidation state of the ferrocene moiety. Gene transfection capability was assayed in terms of EGFP expression using pEGFP-C3 plasmid DNA in three cancer cell lines of different origin, namely Caco-2, HEK293T and HeLa in the presence of serum. Figure 4. Effect of oxidation state of ferrocene on maximum transfection efficacies of monomeric and gemini lipids in three different cell lines (Caco-2, HEK 293T and HeLa). Cationic liposomal formulations with ferrocene in its reduced state were observed to be potent transfectants reaching the EGFP expression levels even better than commercial lipofectamine 2000 in the presence of serum as evidenced by flow cytometry. EGFP expression was further substantiated using fluorescence microscopy studies. All liposomal formulations containing oxidized ferrocene displayed diminished levels of gene expression and interestingly, these results were consistent for each formulation in all the three cell lines. Assessment of EGFP expression mediated by both reduced and oxidized ferrocene containing formulations was also undertaken following cellular internalization of labelled pDNA using confocal microscopy and flow cytometry. Lipoplexes derived from different liposomal formulations with reduced and oxidized ferrocene were characterised using TEM, AFM, zeta potential and DLS measurements. Overall, we demonstrate here controlled gene transfection levels using redox driven, transfection efficient cationic monomeric and gemini lipids. Chapter 5: Synthesis of ‘Click Chemistry’ Mediated Glycolipids: Their Aggregation Properties and Interaction with DPPC Membranes This chapter describes the synthesis and aggregation properties of cholesterol based glycolipids along with their interaction with a model phosphatidylcholine membranes. Three series of non-ionic glycolipids with hydrophobic cholesterol backbone and various monosaccharide and disaccharide sugars as the hydrophilic polar domain have been synthesized. These were conjugated to the cholesteryl backbone via oligooxyethylene spacers of different lengths (n = 1, 3 and 4) using Cu (I) catalyzed Huisgen [3+2] cycloaddition, which is popularly known as „Click Chemistry‟. All the synthetic glycolipids (5a-d, 6a-d and 7a-d) formed vesicular aggregates in aqueous medium as confirmed by TEM and DLS. XRD studies with the cast films of lipids revealed that the bilayer width increased with increase in the length of oligoethylene spacer unit that has been incorporated between the hydrophobic and hydrophilic domains. Also, within the same series containing a particular oligoethylene unit, bilayer widths were found to be more for the lipids containing disaccharides as their headgroup than monosaccharides. Figure 5. Molecular structures of various cholesterol-based glycolipids. Calorimetry studies of the coaggregates containing naturally occurring 1, 2-dipalmitoylphosphatidylcholine (DPPC) and various mol-% of each of the glycolipids revealed that more than 30 mol-% of glycolipids are required to completely abolish the phase transition of DPPC membranes. These results were further supported by fluorescence anisotropy measurements of the co-aggregates using 1, 6-diphenylhexatriene (DPH) as a probe. Fluorescence anisotropy of the neat vesicles revealed that 9a and 9c were more rigid than DPPC vesicles in the solid-like gel phase, while the glycolipids with longer oxyethylene spacers (n = 3 and 4) were less rigid than the DPPC vesicles. Chapter 6. Hydrophobic Moiety Decides the Synergistic Increase in Transfection Efficiency in Cationic Phospholipid/Cationic Lipid mixtures This chapter describes the effect of inclusion of cationic lipid/cationic gemini lipids into the membranes of a cationic phospholipid on the gene delivery efficiency across HeLa and HEK293T cell lines. Although all the three cationic lipids have the same quaternary ammonium moiety as their headgroup, they differ from each other in terms of their hydrophobic moiety and in the number of cationic headgroups. Chol-N is a cholesterol based monocationic lipid, while 2C14-N and 2C14N-5-N2C14N are monomeric and gemini cationic lipids respectively with pseudoglycerol backbone consisting of tetradecyl (n-C14H29) chains. Each of the three cationic lipids under the current investigation, namely, Chol-N, 2C14-N and 2C14N-5-N2C14N were added in different ratios to EtDMoPC and the resultant mixed membranes were studied for the biophysical characterization and gene delivery efficacies. Figure 6. Molecular structures of cationic lipids used in this study. All the formulations were characterized using dynamic light scattering and zeta potential measurements to obtain their hydrodynamic diameters and surface charge properties respectively. Their DNA binding ability was also studied by measuring changes in zeta potential and gel electrophoresis of the lipoplexes formed by the coliposomal formulations and pDNA at different Lipid/DNA weight ratios. The gene delivery efficacies of various formulations were studied in terms of EGFP expression using pEGFP-C3 plasmid DNA in two different cell lines, namely HeLa and HEK293T. In the absence of serum we found that the formulation (EtDMoPC+2C14N-5-N2C14N) showed better transfection efficiency than the individual lipids. However, in the case of others, i.e., (EtDMoPC+Chol-N) and (EtDMoPC+2C14-N) formulations, there was a slight decrease in transfection efficiency compared to the individual lipids. In the presence of serum, the formulations (EtDMoPC+2C14-N) and (EtDMoPC+2C14N-5-N2C14N) showed significantly higher transfection efficacies compared to their individual lipids. Fusion assay using labelled cationic lipid formulations and unlabelled anionic liposomes revealed that lipoplexes prepared from EtDMoPC+ 2C14-N and EtDMoPC+ 2C14N-5-N2C14 exhibited much higher fusogenicity as compared to the lipoplexes prepared using EtDMoPC+Chol-N as well as the individual lipids. Thus, the liposome formulations which showed better transfection activity fused more readily with the anionic liposomes than did the formulations with poorer activity. Overall, we found that the hydrophobic domain of the cationic lipid/cationic gemini lipid that is added to cationic phospholipid has an important role on the transfection efficiency of the mixed formulations. Additionally the cytotoxicity studies revealed that each of these formulations was not significantly toxic making them viable for applications in vivo. (For structural formula pl see the abstract pdf file)

The thesis entitled “Novel Redox Responsive Cationic Lipids, Lipopolymers, Glycolipids and Phospholipid-Cationic Lipid Mixtures: Syntheses, Aggregation and Gene Transfection Properties” elucidates the design, synthesis, aggregation and gene transfection properties of novel cholesterol based cationic lipids with ferrocene as the redox moiety, polyethylenimine based ferrocenylated lipopolymers and cholesterol based non-ionic glycolipids. The thesis also discusses the cationic phospholipid-cationic lipid mixtures as superior gene transfection agents. The work has been divided into six chapters. Chapter 1. Introduction Part A. Various Cholesterol based Systems for Applications as Biomaterials Liposomes composed of cationic lipids have become popular gene delivery vehicles. A great deal of research is being pursued to make efficient vectors by varying their molecular architecture. Cholesterol being ubiquitous component in most of the animal cell membranes is increasingly being used as a hydrophobic segment of synthetic cationic lipids. In this chapter we describe various cholesterol based cationic lipids and focus on the effect of modifying various structural segments like linker and the headgroup of the cationic lipids on gene transfection efficiency with a special emphasis on the importance of ether linkage between cholesteryl backbone and the polar headgroup. Interaction of cationic cholesteryl lipids with dipalmitylphosphatidycholine membranes is also discussed here. Apart from cholesterol being an attractive scaffold in the drug/gene delivery vehicles, certain cholesteryl derivatives have also been shown to be attractive room temperature liquid-crystalline materials. Part B. Diverse Applications of Ferrocene Derivatives This chapter gives a brief overview of ferrocene chemistry followed by description of major applications of ferrocenyl derivatives in a variety of fields like catalysis, materials chemistry, electrochemical sensors, medicinal chemistry etc. We discuss the use of ferrocene as an electrochemical and redox active switch to achieve control over supramolecular aggregation. It also reviews ferrocene based amphiphiles including surfactants, lipids and polymers with an emphasis on the role of ferrocene over aggregate formation and their utilization in biological applications. Chapter 2: Optimization of Redox Active Alkyl-Ferrocene Modified Polyethylenimines for Efficacious Gene Delivery in Serum 1a-c, n = 6, P8-C6-F1, P8-C6-F2, P8-C6-F3 2a-c, n = 11, P8-C11-F1 P8-C11-F2, P8-C11-F3 % ferrocene grafting, F1 = 15%, F2 = 25% and F3 = 50% Figure 1. Structure of the alkyl-ferrocene modified 800 Da Branched Polyethylenimine. In this chapter we present six new lipopolymers based on low molecular weight polyethylenimines (BPEI 800 Da) which are hydrophobically modified using ferrocene terminated alkyl tails of variable lengths. The effects of degree of grafting, spacer length and redox state of ferrocene in the lipopolymer on the self assembly properties were investigated in detail by transmission electron microscopy (TEM), atomic force microscopy (AFM), dynamic light scattering (DLS) and zeta potential measurements. The assemblies displayed a redox induced increase in the size of the aggregates. The coliposomes comprising of the lipopolymer and a helper lipid 1,2-Dioleoyl-sn-glycero-3-phosphatidylethanolamine (DOPE) showed excellent gene delivery capability in serum containing environment in two cancer cell lines (HeLa, U251 cells). Optimized formulations showed remarkably higher transfection activity than BPEI 25 KDa and even better than commercial Lipofectamine 2000 as evidenced from luciferase activity and EGFP expression analysis. Oxidation of ferrocene in lipopolymers led to reduced levels of gene transfection which was also followed by cellular internalization of fluorescently labeled pDNA using confocal microscopy. Cytotoxicity assay revealed no obvious toxicity for the lipopolyplexes in the range of optimized transfection levels. Overall, we have exploited the redox activity of ferrocene in PEI based polymeric gene carriers for trenchant control over gene transfection potential. RLU/mg protein HeLa Cells Figure 2. Maximum transfection efficacies of optimized redox lipopolymer/DOPE formulations by (A) Luciferase Assay and (B) Flow cytometry (GFP expression). Chapter 3. Membranes derived from Redox-active Cholesterol based Cationic Lipids and their Interactions with DNA and Phospholipid Membranes Figure 3. Molecular structures of the electroactive cholesterol based monomeric and gemini lipids. This chapter describes the synthesis and aggregation properties of two series of redox-active ferrocene containing monomeric and gemini cationic lipids with cholesterol as a hydrophobic domain. These cationic lipids are modified at their headgroup region using ferrocene terminated alkyl chains of differing length. All the four cationic lipids formed stable suspensions in water. Aggregation behavior of these cationic lipids in aqueous suspensions in their unoxidized and oxidized state was studied using TEM, DLS, zeta potential measurements and XRD studies. Cationic lipids with ferrocene in natural, reduced state were found form bigger sized vesicles which upon oxidation became smaller aggregates with increased zeta potential. XRD results indicate the existence of nice lamellar arrangements of the lipid bilayers. Thermotropic phase transition behavior of DPPC membranes incorporated with cationic ferrocene lipids was also studied using differential scanning calorimetry. Finally, we assayed pDNA (plasmid DNA) binding ability of all the four cationic lipids using ethidium bromide intercalation assay where all the cationic lipid formulations showed excellent DNA binding capability. In the experiments involving SDS-induced release of DNA, we observed that redox-active monomeric lipids (3a-b) were found to be more efficient in facilitating the release of DNA from the liposome-DNA complex in the presence of negatively charged SDS micelles than their gemini counterparts (4a-b). Chapter 4. Redox-responsive Gene Delivery by Ferrocene containing Cationic Cholesteryl Lipids in Serum This chapter describes the transfection efficacy of redox-active monomeric and gemini cationic lipids with cholesterol backbone. The transfection efficiency of all the lipids could be tuned by changing the oxidation state of the ferrocene moiety. Gene transfection capability was assayed in terms of EGFP expression using pEGFP-C3 plasmid DNA in three cancer cell lines of different origin, namely Caco-2, HEK293T and HeLa in the presence of serum. Figure 4. Effect of oxidation state of ferrocene on maximum transfection efficacies of monomeric and gemini lipids in three different cell lines (Caco-2, HEK 293T and HeLa). Cationic liposomal formulations with ferrocene in its reduced state were observed to be potent transfectants reaching the EGFP expression levels even better than commercial lipofectamine 2000 in the presence of serum as evidenced by flow cytometry. EGFP expression was further substantiated using fluorescence microscopy studies. All liposomal formulations containing oxidized ferrocene displayed diminished levels of gene expression and interestingly, these results were consistent for each formulation in all the three cell lines. Assessment of EGFP expression mediated by both reduced and oxidized ferrocene containing formulations was also undertaken following cellular internalization of labelled pDNA using confocal microscopy and flow cytometry. Lipoplexes derived from different liposomal formulations with reduced and oxidized ferrocene were characterised using TEM, AFM, zeta potential and DLS measurements. Overall, we demonstrate here controlled gene transfection levels using redox driven, transfection efficient cationic monomeric and gemini lipids. Chapter 5: Synthesis of ‘Click Chemistry’ Mediated Glycolipids: Their Aggregation Properties and Interaction with DPPC Membranes This chapter describes the synthesis and aggregation properties of cholesterol based glycolipids along with their interaction with a model phosphatidylcholine membranes. Three series of non-ionic glycolipids with hydrophobic cholesterol backbone and various monosaccharide and disaccharide sugars as the hydrophilic polar domain have been synthesized. These were conjugated to the cholesteryl backbone via oligooxyethylene spacers of different lengths (n = 1, 3 and 4) using Cu (I) catalyzed Huisgen [3+2] cycloaddition, which is popularly known as „Click Chemistry‟. All the synthetic glycolipids (5a-d, 6a-d and 7a-d) formed vesicular aggregates in aqueous medium as confirmed by TEM and DLS. XRD studies with the cast films of lipids revealed that the bilayer width increased with increase in the length of oligoethylene spacer unit that has been incorporated between the hydrophobic and hydrophilic domains. Also, within the same series containing a particular oligoethylene unit, bilayer widths were found to be more for the lipids containing disaccharides as their headgroup than monosaccharides. Figure 5. Molecular structures of various cholesterol-based glycolipids. Calorimetry studies of the coaggregates containing naturally occurring 1, 2-dipalmitoylphosphatidylcholine (DPPC) and various mol-% of each of the glycolipids revealed that more than 30 mol-% of glycolipids are required to completely abolish the phase transition of DPPC membranes. These results were further supported by fluorescence anisotropy measurements of the co-aggregates using 1, 6-diphenylhexatriene (DPH) as a probe. Fluorescence anisotropy of the neat vesicles revealed that 9a and 9c were more rigid than DPPC vesicles in the solid-like gel phase, while the glycolipids with longer oxyethylene spacers (n = 3 and 4) were less rigid than the DPPC vesicles. Chapter 6. Hydrophobic Moiety Decides the Synergistic Increase in Transfection Efficiency in Cationic Phospholipid/Cationic Lipid mixtures This chapter describes the effect of inclusion of cationic lipid/cationic gemini lipids into the membranes of a cationic phospholipid on the gene delivery efficiency across HeLa and HEK293T cell lines. Although all the three cationic lipids have the same quaternary ammonium moiety as their headgroup, they differ from each other in terms of their hydrophobic moiety and in the number of cationic headgroups. Chol-N is a cholesterol based monocationic lipid, while 2C14-N and 2C14N-5-N2C14N are monomeric and gemini cationic lipids respectively with pseudoglycerol backbone consisting of tetradecyl (n-C14H29) chains. Each of the three cationic lipids under the current investigation, namely, Chol-N, 2C14-N and 2C14N-5-N2C14N were added in different ratios to EtDMoPC and the resultant mixed membranes were studied for the biophysical characterization and gene delivery efficacies. Figure 6. Molecular structures of cationic lipids used in this study. All the formulations were characterized using dynamic light scattering and zeta potential measurements to obtain their hydrodynamic diameters and surface charge properties respectively. Their DNA binding ability was also studied by measuring changes in zeta potential and gel electrophoresis of the lipoplexes formed by the coliposomal formulations and pDNA at different Lipid/DNA weight ratios. The gene delivery efficacies of various formulations were studied in terms of EGFP expression using pEGFP-C3 plasmid DNA in two different cell lines, namely HeLa and HEK293T. In the absence of serum we found that the formulation (EtDMoPC+2C14N-5-N2C14N) showed better transfection efficiency than the individual lipids. However, in the case of others, i.e., (EtDMoPC+Chol-N) and (EtDMoPC+2C14-N) formulations, there was a slight decrease in transfection efficiency compared to the individual lipids. In the presence of serum, the formulations (EtDMoPC+2C14-N) and (EtDMoPC+2C14N-5-N2C14N) showed significantly higher transfection efficacies compared to their individual lipids. Fusion assay using labelled cationic lipid formulations and unlabelled anionic liposomes revealed that lipoplexes prepared from EtDMoPC+ 2C14-N and EtDMoPC+ 2C14N-5-N2C14 exhibited much higher fusogenicity as compared to the lipoplexes prepared using EtDMoPC+Chol-N as well as the individual lipids. Thus, the liposome formulations which showed better transfection activity fused more readily with the anionic liposomes than did the formulations with poorer activity. Overall, we found that the hydrophobic domain of the cationic lipid/cationic gemini lipid that is added to cationic phospholipid has an important role on the transfection efficiency of the mixed formulations. Additionally the cytotoxicity studies revealed that each of these formulations was not significantly toxic making them viable for applications in vivo. (For structural formula pl see the abstract pdf file)

The thesis presents detailed results of theoretical analyses based on extensive computer simulation studies with an aim to explore, quantify whenever possible, and understand the collective excitations, relaxation processes and temperature dependent phase separation kinetics in several binary mixtures. We also investigate the structure and dynamics of water in the vicinity of several biologically active proteins and small hydrophobes. Based on the phenomena studied the thesis has been divided into four major parts I. Collective excitations and ultrafast solvation dynamics in binary mixtures II. Non-equilibrium solvation dynamics in binary mixture: Composition dependence of non-linear relaxation III.Nanoscale heterogeneous phase separation kinetics in binary mixtures: Multistage dynamics IV.Spatial dependence of dielectric constant in protein-water systems and hydrophobic hydration driven self-assembly of hydrophobic molecules in water: Role of nucleation

碩士
國立高雄大學
資訊工程學系碩士班
105
Human action recognition has been a very important topic in computer vision and image processing. In this thesis, we present a human action recognition system using the Gaussian mixture background model, morphological processing, motion energy image and template matching. First, we detect human and extract human contour in a video according to the Gaussian mixture background model. After the human contour is extracted, we reduce the noise in human contour by using Gaussian blur. Then we use the erosion and dilation of morphological processing to connect the broken contour area .We remove the other nonhuman targets in the background by calculating to the maximum contour area. Second, in order to set up the motion energy image, we align the centroid in the motion energy image after calculating the coordinate of the centroid in human contour. Finally, according to the three templates selected in advance, we can complete the human action recognition using template matching method. Experiments by three-fold cross validation showed that the accuracy of our human action recognition is 91.4%. Most errors are due to different walking sizes between humans.

碩士
國立暨南國際大學
應用材料及光電工程學系
104
The aim of this thesis is to study the effects of adding different nanoparticles (NPs) and ZnO nanorods (NRs) on the current-voltage (IV) and switching characteristics of metal/insulator/ZnO NRs/metal RRAM device using a polystyrene (PS) and poly (N- ethyl-2-vinyl carbazole) (P2VK) mixture as active layer. We found that a mixture of PS and 4 weight percent of P2VK could improve the stability of the device as well as increase the device yield. Adding different materials of NPs could effectively enhance the bond strength of the film and reduce the leakage as well as the operating currents. Device with the TiO2 NPs showed better switching characteristics. Experimental results showed that all the hetrojunction structures of metal/insulator/ZnO NRs/metal devices exhibited the diode IV characteristics with different current levels in positive and negative biases. Adding different materials of NPs affected the magnitude of current levels in the positive bias region. Hysteresis was observed nearly for all the IV curves. It was found that IV curves of PS/ P2VK composite mixed with TiO2 NPs exhibited the largest hysteresis. We also found that the initially counterclockwise (clockwise) hysteresis loops of the IV curves might become clockwise (counterclockwise) after a long time placement. After a 1000 sec data retention test, the PS/ P2VK composite mixed with TiO2 NPs showed the best data retention performance, which was consistent with the hysteresis behavior of the IV curves. Analysis of the hytrojuction energy band diagram for the metal/insulator/ZnO NRs/metal structure showed an energy well of hole in the PS/ZnO interface. The barrier height of the hole well is about 0.8 eV. However, the potential barrier of the conduction electron is about 2.5 eV. It was believed that the holes dominated the current conduction mechanism. We reasonably assumed that the change of barrier height caused by biasing was mainly in PS side, then the diode IV behavior could well explained. Because the presence of hole potential well, it was believed that the accumulated holes capture and release near the PS/ZnO NRs interface with ultra-large surface area caused the hysteresis of the IV curves. Adding NPs (TiO2) might increase the trapping centers and possibility of holes capture and release near the PS/ZnO NRs interface region, resulting in a larger hysteresis. It was consistent with a larger hysteresis was observed in adding the TiO2 NPs. We suggested that the memory characteristics of the devices attributed to the holes capture and release near the PS/ZnO NRs interface region Key words: RRAM, polystyrene, poly (N- ethyl-2-vinyl carbazole), nanoparticles, nanorods.

While a number of different proteomic, genomic, and computational approaches exist for the characterization of drug action, each of the experimental approaches developed to date has both strengths and weaknesses. Currently, there is no one "perfect" assay for drug mode-of-action studies. A protocol that could assay all the proteins in the proteome for both direct and indirect binding interactions of drugs would greatly facilitate studies of drug action. Recently, the SPROX (stability of proteins from rates of oxidation) technique was developed as a chemical modification- and mass spectrometry-based strategy for detecting protein-ligand interactions by monitoring the change in thermodynamic stability of proteins upon ligand binding. This is accomplished by monitoring the denaturant dependent oxidation of globally protected methionine residues. The SPROX technique has been interfaced with bottom-up proteomics methods to allow for the proteome-wide analysis of protein-ligand interactions. However, the strategy has been limited by the need to detect and quantify methionine containing peptides in the bottom-up proteomics experiment.

The work in this dissertation is focused on evaluating the current SPROX protocol, developing modifications to improve proteome coverage, and applying the SPROX platform to two different drug mode-of-action studies. Three main strategies were employed to improve protein coverage. First, a chemo-selective isolation of un-oxidized methionine containing peptides was employed to enrich for methionine containing peptides, and it was found to produce a ~2-fold improvement in proteomic coverage. Second, a pre-fractionation strategy involving the use of isoelectric focusing was employed to decrease sample complexity prior to LC-MS/MS analysis and it was found to generate a ~2-3 fold improvement in proteomic coverage, however when combined with the methionine enrichment strategy the improvement was ~6-fold as the benefits of both were additive. Third, a tryptophan modification strategy was developed that could ultimately expand the number of useful peptides in proteome-wide SPROX experiments to include those that contain tryptophan. Also, investigated was the use of several different mass spectrometer systems (including a bench-top quadrupole and orbitrap system and two different quadrupole time-of-flight systems) in the SPROX protocol. The results of these studies indicate that there is a significant advantage in proteome coverage when faster mass spectrometers are used. The use of high energy collision dissociation (HCD) in the orbitrap system was also more advantageous than the use of collision induced dissociation (CID) in the Q-ToF systems. Regardless of the mass spectrometer used, the major source of error in the SPROX experiment was found to be the random error associated with the LC-MS/MS analysis of isobaric mass tagged peptides. This random error was found to yield a false discovery rate of between 3 and 10% for "hit" peptides in the SPROX experiment.

The above improvements in the SPROX protocol were used in two protein-ligand binding experiments. One set of experiments involved studies on two small molecules with a specific anti-cancer phenotype in human colon cancer cells. These studies identified 17 proteins as potential "hits" of these two small molecules. After preliminary validation of these proteins, approximately 50% were eliminated as false positives and one protein, p80/nucleophosim, showed consistent data indicating a destabilizing interaction with both small molecules. The destabilization is indicative of an indirect interaction with the small molecules that would be mediated through a protein-protein interaction network. In another set of experiments the breast cancer drug, tamoxifen, and its main, active metabolite, 4-hydroxy tamoxifen, were assayed for binding to the proteins in a yeast cell lysate to better understand its adverse effects on yeast cells. The results of these studies identified ~80 proteins as potential "hits" of these two drugs. After preliminary validation of these proteins, approximately 30% were eliminated as false positives and one protein, SIS1, type II Hsp40, showed consistent data indicative of a direct binding interaction.

Dissertation

碩士
大同大學
化學工程學系(所)
100
The aim of the research work was intended to study the effect of terminal chiral chain moiety on the mesophases. By means of compound, 4-(4-Hydroxyphenyl)benzoic acid (R0) as building block, six homologous series of liquid crystal materials comprised of different chiral chains were synthesized for investigating the correlation between the chemical structure of chiral tails and mesomorphic properties. The first part is to investigate the effect of lengthening the terminal chain on the formation of mesogenic phase for the chiral swallow-tailed compounds I(m=1-3) possessing intramolecular hydrogen bonding between the hydroxyl and ester group. Series of I only have cholesteric LC (N*) phase in cooling process. I(m=2) have the widest temperature range as large as 29.1°C. Second part is the chiral T-shaped compounds, II (n=5, m=2) T5 and II (n=5, m=3) T7 display enantiotropic mesophases of Iso., SmA* and Cr. phases whereas the other compounds have no mesophases in cooling process. An increasing chiral chain length (m) or the spacer length between cyano-biphenyl moiety and phenyl core (n) don’t obviously affect on the formation of mesogenic phase for these compounds. In addition, when the length of the chiral swallow-tailed chain is shorter or the spacer length bwtween cyano-biphenyl moiety and phenyl core is longer, these T-shaped molecules exhibits no mesophase. Only T5 and T7 have SmA* phase in cooling process. Compound T5 exhibits the wider temperature range of SmA* as large as 46.4°C. The third part of the work is to prepare binary mixtures of chiral swallow-tailed compound I(m=2) and chiral dopants S811, N821 and E821 which were synthesized by our laboratory. The structures of chiral dopants are shown below, in order to investigate the effect of chiral dopants upon the chiral swallow-tailed compounds I(m=1-3) on the formation of mesogenic phase. In this series binary mixtures, the ratio of S811 don’t directly influence the formation of TGBA* phase. On the other hand, compound I(m=2) doped with N821 and E821 for the formation of TGBA* phase is apparent. Especially, when the ratio of dopants between 10% and 20%, such as the proportion of 80 % I (m=2) and 20 % E821 has the widest temperature range of TGBA* phase in this series. When the dopant is N821 or E821, the temperature range of N* phase is depressed as the dopant increases. Conversely, the temperature range of SmA* phase is increased as the dopant increases.

Pharmaka werden nach ihrer Einnahme bzw. Verabreichung über verschiedene Pfade in die Umwelt eingetragen. Obwohl Arzneimittel zu den toxikologisch best-untersuchten und -charakterisierten Stoffen gehören, ist ihre Wirkung auf die Umwelt und die darin lebenden Organismen weit weniger gut untersucht. Wenn in der Literatur Daten zur Ökotoxizität vorhanden sind, so beziehen sich diese meist nur auf die Wirkung von Einzelstoffen. In der Umwelt sind die Organismen jedoch gegenüber Mischungen exponiert. Aufgrund der geschilderten Problematik wurden eine Reihe von Arzneimitteln unterschiedlicher Indikationsgruppen einzeln und in Kombination mit dem Embryotest mit dem Zebrabärbling (Danio rerio, DarT) untersucht. Dieses Testsystem wurde durch Schulte & Nagel (1994) als Alternativmethode zum akuten Fischtest nach OECD 203 entwickelt und bietet den Vorteil neben letalen auch eine Reihe von subletalen Endpunkten erfassen zu können. Es handelt sich zudem nach dem deutschen Tierschutzgesetz nicht um einen Tierversuch. Die generelle Vergleichbarkeit der ermittelten Werte mit Daten aus akuten Fischtests nach OECD 203 sowie die Anwendbarkeit für verschiedenste Fragestellungen konnten in einer Reihe von Studien gezeigt werden (Nagel, 2002). Für die hier vorgestellten Untersuchungen wurden zunächst 32 Pharmaka und drei Pflanzenschutzmittel als Einzelstoffe mit dem DarT untersucht. Basierend auf den Ergebnissen der Einzelstofftests wurden Mischungen sowohl aus Substanzen mit ähnlichen als auch unähnlichen Wirkmechanismen getestet. Es zeigte sich, dass unabhängig vom Wirkmechanismus die Mischungstoxizität durch das Konzept der Konzentrationsadditivität gut vorhergesagt wurde, während das Konzept der Unabhängigen Wirkung die Mischungstoxizität unterschätzte. Ebenfalls konnte gezeigt werden, dass die Kombination der Stoffe auf Basis der NOEC, die im DarT anhand der Herzschlagfrequenz nach 48 Stunden ermittelt wird, zu deutlichen Mischungseffekten führt.