Previous studies from our lab have shown that Activating protein-2 (AP-2) transcription factors, AP-2α and AP-2β are important in retinal development, specifically in the developing horizontal and post-mitotic amacrine cells. Conditional deletion of AP-2α and AP-2β from the retina of mice resulted in a variety of abnormalities including loss of horizontal cells, defects in the photoreceptor ribbons in which synapses failed to form, along with evidence that amacrine cell mosaic patterning may be disrupted. The current thesis examined the neural retina of these AP-2α and AP-2β conditional mice in greater detail using immunofluorescence of histological sections and whole retinas, and electroretinograms to measure retinal function in post-natal adult mice. Examining regularity of the amacrine cell mosaics of these double mutants showed the loss of AP-2α and AP-2β led to significant irregularities in the mosaic patterning of these cells as determined by Voronoi domain areas (P<0.01) and nearest-neighbour distances (P<0.03). No significant changes in amacrine population numbers were observed. Observed cellular changes in the double conditional knock out mice were reflected as a change in the retinal response to light as recorded by electroretinograms. For example, the b-wave amplitude, representative of the interneuron signal processing, was significantly affected in those mice lacking AP-2⍺ and AP-2β (P<0.0001). Taken together, the work presented in this thesis implicates the requirement of AP-2⍺ and AP-2β for the correct amacrine mosaic patterning and for the proper functional light response in the retina. / Thesis / Master of Applied Science (MASc)

An investigation into the feasibility of laser ablation as a material selective removal technique was conducted. Polyimide films approximately 1 micron thick were prepared on silicon wafers. The ablation rate of these films as a function of laser fluence was studied. It was observed that a minimum threshold fluence of 67 +/- 6 mJ/cm^2 had to be surpassed to achieve a significant material removal rate. In addition to polyimide, the removal and damage characteristics of aluminum films were also examined. These films, which ranged in thickness from 50 to 1000 nm, were deposited on polyimide coated silicon wafers. It was found that the best results were produced by a single shot removal technique, with the quality of the hole dependent upon the incident fluence. At lower fluences, removal ceased and only physical damage to the film occurred. In an attempt to characterize this damage, the electrical resistance of small aluminum wires was monitored as they were exposed to laser pulses. It was found that a change in the resistance of the wires could not be detected prior to the onset of visible damage. Once the optimal removal fluences for both materials were determined, a multilayer consisting of an aluminum layer "sandwiched" between two polyimide layers was prepared. By varying only the incident fluence, it was possible to remove upper layers without removing or damaging the underlying ones. In a related experiment, the possible incubation of polyimide by low fluence laser pulses was also examined. / Thesis / Master of Engineering (ME)

The development of nanoscale patterns has a vast variety of applications going from biology to solid state devices. In this research we present a new direct patterning technique in which laser photoreduction of silver from a liquid is controlled by a scanning atomic force microscope tip. While pursuing the formation of patterns using the plasmonic field enhancement of an electromagnetic wave incident on a metallic Atomic Force Microscope (AFM) tip, our group discovered that contrary to expectations, the tip suppresses, rather than enhances, deposition on the underlying substrate, and this suppression persists in the absence of the tip. Experiments presented here exclude three potential mechanisms: purely mechanical material removal, depletion of the silver precursor, and preferential photoreduction on existing deposits. An example of a nano-scaled pattern was generated to show the possibilities of this work. These results represent a first step toward direct, negative tone, tip-based patterning of functional materials.

La réduction des dimensions des dispositifs et les limites atteintes par la lithographie pour les nœuds technologiques sub-20nm requièrent l’introduction d’un « double patterning » pour définir les contacts. Le masque final est défini par l’intersection d’un masque dur en TiN et d’un masque organique (OPL) et est utilisé pour transférer les motifs des contacts par gravure plasma dans une couche de diélectriques (SiO2/Si3N4). Par rapport aux nœuds technologiques précédents, cette architecture entraine de nouvelles problématiques dues à l’intégration du double patterning et du masque dur en TiN.Cette thèse porte sur la gravure des contacts définis par « double patterning » pour la technologie 14 nm FDSOI (Fully Depleted Silicon On Insulator) à STMicroelectronics. Plus particulièrement, l’objectif principal de ce travail de thèse a été d’évaluer l’effet des masques d’OPL et de TiN sur la gravure des contacts en termes de contrôle dimensionnel (CD) et de profil de gravure. Dans cet objectif, nous avons comparé deux procédés de gravure de l’OPL à base de N2/H2 ou de COS/O2 et leur impact sur le transfert des contacts. Un autre objectif de ce travail de thèse a été consacré à la compréhension et à la limitation du phénomène de croissance de résidus métalliques après le procédé de gravure des contacts. Ceci est obtenu notamment à travers le développement de traitements plasma post gravure. Pour déterminer les mécanismes d’interactions entre les plasmas du procédé de gravure des contacts et les matériaux des masques, des analyses de la surface des matériaux exposés aux plasmas ont été réalisées par des techniques telles que l’XPS et l’EDX et des analyses de la phase gazeuses du plasma ont été réalisées par spectroscopie d’émission optique (Optical Emission Spectroscopy – OES). Nous avons montré que les profiles des contacts étaient influencés par le procédé de l’étape d’ouverture de l’OPL et particulièrement à travers l’interaction des plasmas et du masque dur en TiN. Cette interaction peut conduire à une modification de la forme du masque dur en TiN et au redépôt de composés métalliques peu volatils sur la plaque et sur les parois du réacteur au cours du procédé de gravure. Ceci peut conduire à une déformation des profils et à un quasi-arrêt de la gravure pendant la gravure des matériaux diélectriques. Par ailleurs, nous avons montré que l’efficacité des traitements à base de méthane pour ralentir ou éviter la croissance de résidus à la surface du TiN après la gravure des diélectriques peut être améliorée par un contrôle de l’état des parois de la chambre au cours du traitement, en effectuant un nettoyage de la chambre en oxygène avant l’application du traitement. / Due to the reduction of the transistor dimensions and the limitations of the lithography to define small contact patterns for the sub-20nm technological nodes, the introduction of double patterning strategies is required for contact patterning. In such architectures, the final mask is defined by the combination of a TiN hard mask and an organic (OPL) mask, which defines the contact patterns that will be transferred into the underlying dielectric layers (SiO2/Si3N4). This leads to new challenges for contacts definition, especially because of the integration of double patterning strategies and TiN hard masks which were not present for previous technologies.This study addresses the contact etching process using a double patterning strategy for the 14 nm Fully Depleted Silicon on Insulator (FDSOI) technology. More particularly, the main goal of this work was to evaluate the impact of both TiN and OPL masks on the contact patterning process in terms of dimensions and profiles control. For this, we have compared two different OPL etch processes (N2/H2 and COS/O2) and their impact in the contact pattern transfer in the dielectric layers. In addition, this work was also dedicated to the understanding and limitation of metallic residues growth occurring after the contact etch process. This is carried out especially through the development of post etch plasma treatments.We performed XPS and EDX analyses to determine the mechanisms involved in the interactions between plasma processing steps and the masking materials (TiN, OPL). The plasma gas phase was also analyzed by Optical Emission Spectroscopy (OES).We show that the contact etch profile is influenced by the OPL etching process due to the interactions between the plasma and the TiN hard mask. These interactions may lead to a modification of the hard mask profile and are at the origin of the metallic contamination observed over the patterned wafer or the reactor walls. Due to this contamination, the contact profiles are deformed and the dielectric etch process may be stopped. Finally, we have shown that the state-of-art CH4-based post-etch-treatments introduced to limit the residues growth after dielectric patterning with a TiN mask can be improved by adding an oxygen-based reactor cleaning process before the post-treatment process.

The purpose of this study, based on the third year of a three-year research study, was to examine Grade 6 students’ previously developed abilities to integrate their understanding of geometric growing patterns with graphic representations as a means of further developing their conception of linear relationships. In addition, I included an investigation to determine whether the students’ understanding of linear relationships of positive values could be extended to support their understanding of negative numbers. The theoretical approach to the microgenetic analyses I conducted is based on Noss & Hoyles’ notion of situated abstractions, which can be defined as the development of successive approximation of formal mathematical knowledge in individuals. I also looked to Roschelle’s work on collaborative conceptual change, which allowed me to examine and document successive mathematical abstractions at a whole-class level. I documented in detail the development of ten grade 6 students’ understanding of linear relationships as they engaged in seven experimental lessons. The results show that these learners were all able to grasp the connections among multiple representations of linear relationships. The students were also able to use their grasp of pattern sequences, graphs and tables of value to work out how to operate with negative numbers, both as the multiplier and as the additive constant. As a contribution to research methodology, the use of two analytical frameworks provides a model of how frameworks can be used to make sense of data and in particular to pinpoint the interplay between individual and collective actions and understanding.

Geofiltracija po statiniais bei aplink ar per juos, yra vienas svarbiausių veiksnių, darančių įtaką jų ilgaamžiškumui, patvarumui ir naudojimo sąlygoms. Darbo tikslas- nusausinus priesmėlio, smėlio gruntus jų svoris padidėja, šis svorio padidėjimas yra netoli pamatų duobės esančio grunto apkrovimas papildoma apkrova. Nuo papildomos apkrovos, greta projektuojamo statinio išsivysto papildomos deformacijos, kurios tampa anksčiau statytų statinių papildomų deformacijų priežastimi. Atliekant magistro darbą, spręstas pagrindinis klausimas- kokiais atstumais būtina atlikti geologinius ir hidrogeologinius tyrimus, kad gautume patikimus geofiltracijos proceso parametrus ir išvengtume neigiamų pagrindo deformacijų. Geofiltracijos matematinis modeliavimas atliktas kompiuterine programa PLAFI. / Geofiltration under, around paling and through it is one of the main factors that influence its durability, longevity and condition of use. Geofiltration is proceeding everywhere and always in natural conditions. Thats why it is essential to know its main parameters when projecting, building, using palings so we would be able to avoid to master it to holes of foundation. The purpose of this topic . When we drain sand, sandy loam grounds their weight starts to increase. From additional strain near building that is under construction developes additional strain that becomes the main cause of previously builted paling cracking. To fulfill the purpose of master‘s work topic we have to solve the main problem which is in what distance it is necessary to accomplish geological and hydra- geological research so we would make reliable geofiltration parameters so we would avoid negative base deformations. This designing was accomplished with computer- based programme PLAFI.

Diencephalic development requires the transcription factors Pax6 and Barhl2 in order to proceed correctly. Both genes are necessary for the normal development of the organizer region known as the zona limitans intrathalamica (ZLI). The ZLI goes on to pattern the diencephalon via its secretion of the morphogen Shh, which inhibits the expression of Pax6. These findings suggest that interactions between Pax6, Barhl2 and Shh may be involved in the control of diencephalic development. This project aims to characterise these interactions and investigate their roles. The expression domains of Pax6 and Barhl2 were mapped during the early development of the mouse diencephalon. Qualitative approaches were employed to confirm the high complementarity of their expression domains and obtain evidence of a mutually repressive relationship existing between the two genes. The findings from a quantitative analysis suggested that this inhibition is incomplete within the thalamus. Investigations using the Pax6-null mutant mouse confirmed that in the absence of Pax6 the thalamic Barhl2 expression domain expands beyond the ventricular zone, the site of thalamic neurogenesis. The influence of Shh signalling on the expression of Pax6 and Barhl2 was investigated via a gain-of-function approach utilising in utero electroporation to activate the Shh pathway. This led to a downregulation of both Pax6 and Barhl2 within the thalamus. In Shh loss-of-function experiments drug treatment with the Shh antagonist vismodegib led to an upregulation of Barhl2 and the loss of the GABAergic pTh-R in the Pax6-null mutant thalamus, but not in the wild type thalamus, suggesting that Pax6 and Shh may be required to inhibit Barhl2 in order for GABAergic neurogenesis to proceed. Barhl2 expression was detected in the Shh-null mutant mouse confirming that, in contrast with their homologues in Drosophila, Shh may be expressed downstream of Barhl2. Together these findings have been used to develop a novel model of thalamic development in which Barhl2 induces ZLI development, inhibition of Barhl2 by Pax6 restricts its expansion, and secretion of Shh by the ZLI then goes on to inhibit Pax6 and Barhl2 in the pTh-R while mutual repression between Pax6 and Barhl2 modulates neurogenesis in the more caudal regions of the thalamic neuroepithelium.

The large numbers of neurons that comprise the adult brain display an immense diversity. Repeated divisions of a relatively small pool of neural stem cells generate this neuronal diversity during development. To increase progress towards medical treatments for neurodegenerative diseases, it is of interest to understand both how neural stem cells generate the assortment of neurons and how these neurons come together to form a functional brain. Brain assembly occurs sequentially across time with early events laying the foundation for later events. Drosophila neural stem cells, neuroblasts (NBs), are an excellent model for investigating how neural diversity is generated and what roles early and late born neurons have in shaping the stereotypical adult brain structure. Generation of neural diversity, begins with specifying the diverse population of stem cells, called spatial patterning, and continues with diversifying neurons made from the diverse stem cells, called temporal patterning. Drosophila NBs exhibit both spatial and temporal patterning. Drosophila NBs have three types of division modes: type 0, type I and type II. Type II NBs expand the number of neurons made with progeny that exhibit a transit-amplifying division pattern, similar to that of mammalian outer subventricular zone (OSVZ) progenitors. Additionally, type II NBs exhibit temporal patterning across both the NB and their progeny to generate a large diversity of neurons that populate a conserved region of the brain responsible for many sensory and motor functions, called the central complex. Type II NBs have only been identified and studied during later stages in development, with nothing known about their origin or early divisions. In this dissertation, I describe the early lineages of the type II NBs within the Drosophila embryo. I show that type II NBs and lineages originate early in development, exhibit temporal patterning across both the NB and transit-amplifying progeny, and produce neurons that survive into the adult brain to innervate and potentially serve as a foundation within the adult central complex. Additionally, I explain how live imaging of the developing Drosophila brain can answer questions not easily addressed through other methods.

"The design and development of chemically modified surfaces for bioanalytical applications is presented. Chemical surface modification is demonstrated to be a method to control surface properties on the molecular level by selecting the appropriate substrate, linking chemistry, and terminal group functionality. These systems utilize spontaneous interactions between individual molecules that allow them to self-assemble into larger, supramolecular constructs with a predictable structure and a high degree of order. Applications investigated in this thesis include: surface patterning, switchable surface wettability, and biological sensor devices that combine surface based molecular recognition, electrochemical detection methods, and microfluidics. A multilayered approach to complex surface patterning is described that combines self-assembly, photolabile protecting groups, and multilayered films. A photolabile protecting group has been incorporated into molecular level films that when cleaved leaves a reactive surface site that can be further functionalized. Surface patterns are created by using a photomask and then further functionalizing the irradiated area through covalent coupling. Fluorophores were attached to the deprotected regions, providing visual evidence of surface patterning. This approach is universal to bind moieties containing free amine groups at defined regions across a surface, allowing for the development of films with complex chemical and physico-chemical properties. Systems with photoswitchable wettability were developed by fabricating multilayered films that include a photoisomerizable moiety, cis-/trans- dicarboxystilbene. When this functionality was incorporated into a multilayered film using non-covalent interactions, irradiation with light of the appropriate wavelength resulted in a conformational change that consequently changed the hydrophobicity of the substrate. Methods were investigated to increase the reversibility of the photoswitching process by creating surface space between the stilbene ligands. Utilizing mixed monolayers for spacing resulted in complete isomerization for one cycle, while the use of SAMs with photolabile groups produced surfaces that underwent isomerization for three complete cycles. A microfluidic device platform for ion sensing applications has been developed. The platform contains components to deliver small volumes of analyte to a surface based microelectrode array and measure changes in analyte concentration electrochemically in an analogous method to that used in conventional electrochemical cells. Crown ether derivatives that bind alkali metal ions have been synthesized and tested as ionophores for a multi-analyte device of this type, and the sensing platform was demonstrated to measure physiological relevant concentrations of potassium ions. Advantages of this design include: high sensitivity (uM to mM), small sample volumes (less than 0.1 mL), multi-analyte capabilities (multiple working electrodes), continuous monitoring (a flow through system), and the ability to be calibrated (the system is reusable). The self-assembled systems described here are platform technologies that can be combined and used in molecular level devices. Current and future work includes: photopatterning of gold and glass substrates for directed cell adhesion and growth, the design and synthesis of selective ion sensors for biological samples, multi-analyte detection in microfluidic devices, and incorporating optical as well as electrochemical transduction methods into sensor devices to allow for greater sensitivity and self-calibration."

Nanoscale patterning of organic molecules has received considerable attention in current nanoscience for a broad range of technological applications. In order to provide a viable approach, this thesis describes catalytic stamp lithography, a novel soft-lithographic process that can easily produce sub-100 nm patterns of organic monolayers on surfaces. Catalytic stamps were fabricated through a two-step procedure in which the nanoscale patterns of transition metal catalysts are first produced on SiOx/Si surfaces via the use of self-assembled block-copolymers, followed by the production of the poly(dimethylsiloxane) (PDMS) stamps on top of the as-patterned metals. Simply peeling off the as-formed PDMS stamps removes the metallic nanostructures, leading to the functional stamps. A number of different patterns with various metals were produced from a commercially available family of block copolymers, polystyrene-block-poly-2-vinylpyridine, by controlling the morphology of thin-film templates through the modulation of molecular weights of polymer blocks or solvent vapor annealing. Using these catalytic stamps, hydrosilylation-based catalytic stamp lithography was first demonstrated. When terminal alkenes, alkynes, or aldehydes were utilized as molecular inks, the metallic (Pt or Pd) nanopatterns on catalytic stamps were translated into corresponding molecular arrays on H-terminated Si(111) or Si(100) surfaces. Since localized catalytic hydrosilylations took place exclusively underneath the patterned metallic nanostructures, the pattern formations were not affected by ink diffusion and stamp deformation even at the sub-20 nm scale, while maintaining the advantages of the stamp-based patterning (i.e., large-area, high-throughput capabilities, and low-cost). The concept of catalytic stamp lithography was further extended with other catalytic reactions, and successful nanoscale patterning was performed using hydrogenation (on azide-terminated SiOx surfaces) and the Heck reaction (on alkene- or bromphenyl-terminated SiOx surfaces). A range of nanopatterned surfaces with different chemical functionalities, including thiol, amine, and acid, were created, and they were further modified through appropriate chemical reactions. The potential utility of this simple approach for the construction of a higher degree of nanoarchitectures was suggested.