Unlike most RNA and DNA containing viruses, which induce cytogenetic damage at random sites throughout the human genome, the highly oncogenic adenovirus type 12 is also capable of inducing damage at specific chromosomal sites. Infection of human embryonic retinal or kidney cells with Ad12 results in the induction of heterochromatic gaps at specific (17q21-22, 1p36, 1q21, and 1q42-43) and random sites in the cellular chromosome. Previous work by Durnam et al. (1986) demonstrated that the viral early region 1 (E1) is sufficient for the induction of damage at band 17q21-22. The objective of the present study was to 1) identify the Ad12 E1 gene product(s) required for the induction of aberrations in human diploid cells, and 2) to determine whether the same or different functions are involved in the induction of damage at specific and random sites. To this end, adenovirus type 12/adenovirus type 5 recombinants with hybrid E1 sequences as well as viruses with mutations in the Ad12 E1B genes were used to map the Ad12 E1 function(s) required for the induction of chromosomal aberrations. The results of this study indicate that the expression of E1A proteins is not sufficient for this effect. On the other hand, mutations within the E1B 55Kd protein but not the E1B 19Kd protein were found to affect the ability of the virus to induce both specific and random damage (Schramayr et al., 1990). / Thesis / Master of Science (MS)

Expression of the Simian Virus 40 (SV40) early region in human cells results in the induction of chromosomal aberrations and polyploidy, and in transformation. To understand how genetic damage occurs and what role it plays in transformation, human diploid fibroblasts and embryonic kidney cells were transfected with plasmids encoding wild type or mutant forms of the viral early region, and the neo gene. Clones selected for G418 resistance and expressing viral genes were initially analyzed within 20 cell divisions. The results of this study demonstrate that expression of the SV40 large T antigen is sufficient for the induction of chromosomal damage and ploidy changes, and that small t does not contribute to these processes. Mutant plasmids either lacking the SV40 origin of DNA replication, or encoding a large T mutant defective in its ability to bind the retinoblastoma gene product (Rb) were as proficient as wild type plasmids, indicating that both viral DNA replication and binding of T antigen to Rb are not required for cytogenic damage. On the other hand, preliminary results with a plasmid encoding a T antigen mutant unable to bind the cellular p53 protein suggest that formation fo this complex may be important for cytogenetic damage. This study has also shown that chromosomal aberrations, but not necessarily polyploidy, increase in frequency and complexity upon subculturing of the clones regardless of whether such populations arrest at crisis or yield immortal lines. These results are compatible with the hypothesis that large T antigen destabilizes the cellular genome, and that specific mutations arising from this process may contribute to cell immortalization. / Thesis / Master of Science (MS)

No / Aspheric intraocular lenses (IOLs) are designed to correct spherical aberration in pseudophakic eyes. We predict the benefit from correcting spherical aberration based on simulations and aberrometry of pseudophakic eyes implanted with spherical IOLs. METHODS Ray tracing was performed through a model eye with an equi-biconvex spherical IOL and with a spherical aberration-correcting aspheric IOL. The IOLs were increasingly tilted and/or displaced, and the resulting transverse aberrations of 169 rays were transformed into Zernike coefficients for different pupil sizes. The benefit from correcting spherical aberration at individual mesopic pupils was investigated by canceling in the sets of Zernike coefficients for 41 eyes implanted with a spherical IOL. RESULTS Both the model eye and the real eye data predict that age-related miosis reduces spherical aberration in the eye implanted with a spherical IOL to approximately 1/3 of the spherical aberration at a 6-mm pupil. A reduction of similar magnitude occurs when spherical aberration-induced non-paraxial defocus is corrected by a spectacle lens. For natural mesopic pupils, canceling the Zernike coefficient improved the objective image quality at a rate similar to changing defocus by 0.05 diopters. Average centration and tilt levels diminish the lead of aspheric IOLs over spherical IOLs, depending on the direction of decentration. CONCLUSIONS The benefit from correcting spherical aberration in a pseudophakic eye is limited for some or all of the following reasons: wearing glasses, age-related miosis, tilt and decentration of IOL, small contribution of spherical aberration to all aberrations, and intersubject variability

Many advances have occurred in the field of optical design during the past decade. Some of the newer topics and concepts associated with the design and use of optical systems are complex and require comprehensive understanding of theory, expertise in state-of-the-art technology, and extensive computer simulations. This dissertation focuses on development of practical methods and tools for successful lens design and evaluation of state-of-the-art imaging and illumination systems. The dissertation addresses several current topics in modern optical engineering and utilizes approaches to provide insights into the inner workings of optical systems. Examples of modern mobile camera lenses are provided to show how specific methods can help to better understand these lens designs and to expand the imaging capabilities of miniature camera systems. Two simple but effective real ray tracing methods for correcting chromatic aberrations in imaging systems are described. The proposed methods separate monochromatic and chromatic aberration correction into two independent problems. This two-step approach provides effective alternatives in correcting chromatic aberrations. A number of unique calculations have been performed and some novel and interesting theoretical results, including the fourth-order theory of irradiance changes in axially symmetric optical systems, are reported. The specific relationships between the irradiance distribution and wavefront aberration coefficients to fourth order are derived for the first time. The practical case of relative illumination at the image plane of an optical system is also discussed in some detail.

This thesis describes an analytical approach to the optical design of four-mirror anastigmatic optical systems. In all cases investigated here the object is at infinity. In the introduction the field of reflecting, or "catoptric", optical system design is discussed and given some historical context. The concept of the "simplest possible reflecting anastigmat" is raised in connection with Plate Diagram analysis. It is shown that four-plate systems are in general the simplest possible anastigmats, and that four-plate systems comprised of four spherical mirrors are the last family of "simplest possible reflecting anastigmats" for which the complete solution set remains unknown. In chapter 2 third-order aberration coefficients in wavefront measure are derived in a form that is particularly suitable for Plate Diagram analysis. These coefficients are subsequently used to describe the Plate Diagram, and to detail the application of the Plate Diagram to the survey of all possible solutions for four-spherical-mirror anastigmats. The Plate Diagram technique is also generalized to investigate its use as an optical design tool. In the example given a generalized Plate Diagram approach is used to determine solutions for four-mirror anastigmats with a prescribed first-order layout and a minimum number of conicoids. In chapter 3 results are presented for the survey of four-spherical-mirror anastigmats in which all elements are required to be smaller than the primary mirror. Two novel families of four-spherical-mirror anastigmats are presented and these are shown to be the only examples of four-spherical-mirror systems that exist under the given constraints. Chapter 4 gives an example of the application of Plate Diagram analysis to the design of an anastigmatic system with a useful first-order layout and a minimum number of conicoid mirrors. It is shown that systems with useful first-order layouts and only one conicoid mirror can be obtained using this method. In chapter 5 results are presented of the survey of all remaining four-spherical-mirror anastigmatic systems: that is systems in which elements are allowed to exceed the diameter of the entrance pupil, which includes systems with concave and convex primary mirrors. A wide variety of solutions are presented and classified according to both the underlying geometry of the solutions and the first-order layouts. Of these systems only one has been reported in previously published literature. The results presented in this thesis complete the set of "four-plate" reflecting anastigmats, and it can now be said that all possible solutions for four-spherical-mirror anastigmatic systems have been determined.

Several factors impact the light irradiance and relative illumination produced by a lens system at its image plane. In addition to the cosine-fourth-power radiometric law, image and pupil aberrations, and light vignetting also count. In this paper, we use an irradiance transport equation to derive a closed form solution that provides insight into how individual aberration terms affect the light irradiance and relative illumination. The theoretical results are in agreement with real ray tracing.

Several factors impact the light irradiance and relative illumination produced by a lens system at its image plane. In addition to cosine-fourth-power radiometric law, image and pupil aberrations and light vignetting also count. We use an irradiance transport equation to derive a closed form solution that provides insight into how individual aberration terms affect the light irradiance and relative illumination. The theoretical results are in agreement with real ray tracing. (C) 2016 Society of Photo-Optical Instrumentation Engineers (SPIE)

Les traitements antinéoplasiques peuvent induire des leucémies myéloblastiques (t-LAM). Ces t-LAM présentent des anomalies cytogénétiques spécifiques de l'agent mutagène. Des monosomies 5 ou 7 ou 5q-/7q- se rencontrent après expositions aux alkylants; des translocations équilibrées impliquant souvent la région 11q23, se voient après anti topoisomérases II. Ces anomalies acquises se voient aussi dans des leucémies myéloblastiques de novo (p-LAM) laissant suggérer des mécanismes leucémogènes identiques entre t-LAM et p-LAM. L'utilisation de la CGH array haute résolution permet la mise en évidence d'anomalies cryptiques. 36 patients présentant une t-LAM et 49 atteints d'une p-LAM sont étudiés avec cet outil. Le but est de rechercher des CNA (Copy Number Alteration) au sein des t-LAM et des p-LAM. Les CNA sont regroupées en régions minimales critiques (RMC) pouvant contenir des gènes candidats à la leucémogenèse. Ces résultats sont comparés à des données déjà publiées. Les RMC situées en 5q et en 7q sont encore trop grandes pour définir aisément des gènes candidats. Dans d'autres régions, RUNX1, NF1, ETS2 ou TET2 sont mis en évidence avec des fréquences différentes entre les t-LAM et les p-LAM. Un classement des anomalies génomiques acquises des LAM en 3 groupes est proposé: les anomalies communes aux t-LAM et aux p-LAM, les anomalies essentiellement retrouvées dans les t-LAM ou dans les p-LAM. L'étude du transcriptome et du miRNome a porté sur un petit nombre de patients étudiés en CGH array. L'interprétation des résultats préliminaires reste difficile lorsqu'ils sont comparés aux données génomiques.

Non-small cell lung cancer (NSCLC) constitutes a clinically, histologically, and genetically heterogeneous disease entity that represents a major cause of cancer-related death. Early-stage patients, who undergo surgery with curative intent, experience high recurrence rates and the effect of adjuvant treatment is modest. Prognostic biomarkers would be of particular relevance to guide intensified treatment depending on expected outcome and moreover often infer a biological role in tumourigenesis. This thesis presents a translational study approach to establish a well-characterised NSCLC frozen-tissue cohort and to obtain a profile of each specimen with regard to genome-wide copy number alterations, global gene expression levels and somatic mutations in selected cancer-related genes. Furthermore, the generation of a formalin-fixed, paraffin-embedded tissue microarray enabled validation of findings on the protein level using immunohistochemistry. The comprehensive molecular characterisation, combined with data on clinical parameters, enabled the analysis of biomarkers linked to disease outcome. In Paper I, single nucleotide polymorphism arrays were applied to assess copy number alterations in NSCLC and associations with overall survival in adenocarcinoma and squamous cell carcinoma were described. In Paper II, we evaluated expression levels of selected stromal proteins in NSCLC using immunohistochemistry and the adhesion molecule CD99 was identified as an outcome-related biomarker in two independent cohorts. Paper III presents a strategy for prognostic biomarker discovery based on gene expression profiling, meta-analysis, and validation of protein expression on tissue microarrays, and suggests the putative tumour suppressor CADM1 as a candidate biomarker. In Paper IV, we propose a prognostic role for tumour-infiltrating IGKC-expressing plasma cells in the local tumour microenvironment, indicating an involvement of the humoral immune response in anti-tumor activity. In Paper V, we combined next-generation deep sequencing with statistical analysis of the TP53 database to define novel parameters for database curation. In summary, this thesis exemplifies the benefits of a translational study approach, based on a comprehensive tumour characterisation, and describes molecular markers associated with clinical outcome in NSCLC.

<p>Phase correction has the potential to increase the image quality of real-time 3D (RT3D) ultrasound, especially for transcranial ultrasound. Such improvement would increase the diagnostic utility of transcranial ultrasound, leading to improvements in stroke diagnosis, treatment, and monitoring. This work describes the implementation of the multi-lag least-squares cross-correlation and partial array speckle brightness methods for static and moving targets and the investigation of contrast-enhanced (CE) RT3D transcranial ultrasound.</p><p>The feasibility of using phase aberration correction with 2D arrays and RT3D ultrasound was investigated. Using the multi-lag cross-correlation method on electronic and physical aberrators, we showed the ability of 3D phase aberration correction to increase anechoic cyst identification, image brightness, contrast-to-noise ratio (CNR), and, in 3D color Doppler experiments, the ability to visualize flow. With a physical aberrator, CNR increased by 13%, while the number of detectable cysts increased from 4.3 to 7.7.</p><p>We performed an institutional review board (IRB) approved clinical trial to assess the ability of a novel ultrasound technique, namely RT3D CE transcranial ultrasound. Using micro-bubble contrast agent, we scanned 17 healthy volunteers via a single temporal window and 9 via the sub-occipital window and report our detection rates for the major cerebral vessels. In 82% of subjects, we identified the ipsilateral circle of Willis from the temporal window, and in 65% we imaged the entire circle of Willis. From the sub-occipital window, we detected the entire vertebrobasilar circulation in 22% of subjects, and in 50% the basilar artery. </p><p>We then compared the performance of the multi-lag cross-correlation method with partial array reference on static and moving targets for an electronic aberrator. After showing that the multi-lag method performs better, we evaluated its performance with a physical aberrator. Using static targets, the correction resulted in an average contrast increase of 22.2%, compared to 13.2% using moving targets. The CNR increased by 20.5% and 12.8%, respectively. Doppler signal strength and number of Doppler voxels increased, by 5.6% and 14.4%, respectively, for the static method, and 9.3% and 4.9% for moving targets. </p><p>We performed two successful in vivo aberration corrections. We used this data and measure the isoplanatic patch size to be an average of 10.1°. The number of Doppler voxels increased by 38.6% and 19.2% for the two corrections. In both volunteers, correction enabled the visualization of a vessel not present in the uncorrected volume. These results are promising, and could potentially have a significant impact on public health.</p><p>Lastly, we show preliminary work testing the feasibility of a unique portable dedicated transcranial ultrasound system capable of simultaneous scanning from all three acoustic windows. Such a system would ideally be used in a preclinical setting, such as an ambulance.</p> / Dissertation