Récemment, de nouvelles techniques ont été développées pour la fabrication des réseaux de Bragg à profil complexe. Ces composants photoniques sont utilisés dans plusieurs applications émergentes telles que la compensation de la dispersion pour les systèmes de communication de longue portée, les lasers à fibre, multiplexeurs et détecteurs optiques. Le diagnostic après inscription devrait fournir les informations nécessaires pour l’amélioration de la fabrication des réseaux de Bragg. Nous savons que les propriétés spectrales du réseau de Bragg sont liées au profil d’indice Δn. Les techniques de mesure directes, telles que la diffraction latérale de Krug, permettent de retrouver l’amplitude de modulation d’indice le long du réseau. Cependant, ces techniques sont insensibles aux fluctuations de phase. Une méthode alternative de caractérisation indirecte fondée sur l’algorithme de Layer-Peeling (LP) a été proposée. Toutefois elle ne peut pas être appliquée à la caractérisation des réseaux longs en raison de la propagation du bruit de calcul. Dans cette thèse nous avons présenté une nouvelle technique pour la mesure directe de l’amplitude et de la phase du profil d’indice le long du réseau de Bragg fondée sur la luminescence bleue (LB) induite par l’irradiation UV. Nos résultats expérimentaux de la mesure du profil de modulation d’indice sont en bonne correspondance avec la méthode de Krug. La méthode que nous proposons peut être appliquée à la caractérisation des réseaux longs. Elle permet de retrouver simultanément l’amplitude de modulation d’indice Δnac(z), la fonction du chirp et détecter le changement de l’indice moyen Δndc(z). / N the last decade new techniques were developed for fabrication of sophisticated Fiber Bragg Gratings (FGBs). This has been motivated by the emergence of many applications such as dispersion compensation for long-haul communication systems, DFB fiber lasers, optical add/drop multiplexers, and optical sensors. Post-fabrication diagnostics should provide relevant information to enhance the FBG fabrication process. It is well known that the FBG spectral properties are related to the index profile Δn. Direct measurement techniques, such as the side diffraction method reported by P. Krug, allow determining the index modulation amplitude along the FBG. Nevertheless, these techniques provide no information about phase fluctuations. An alternative method of indirect characterization, based on the Layer-Peeling (LP) algorithm, consists in Bragg grating profile reconstruction from its complex reflectivity. However, the LP method is unstable when applied to characterize long FBGs (>1mm) due to the error propagation effect. In this thesis we have shown the principle of a novel technique for the direct measurement of amplitude and phase variations of the index modulation along an FBG based on the blue luminescence (BL). Our experimental results are in a good agreement with the according Krug characterization. The proposed method of FBG characterization in amplitude and phase using the UV induced BL can be applied to long gratings (up to tens of centimeters) having complex index modulation profiles. It allows retrieving simultaneously the index profile modulation Δnac(z) and the chirp function, localizing phase shifts, and also detecting the mean index change Δndc(z).

This study aims to determine species-level relationships within the genus Heteromys, as well as generic-level relationships among members of the subfamily Heteromyinae using a phylogenetic framework. Molecular sequence data were generated from two mitochondrial genes (cytochrome b and cytochrome oxidase I) and three nuclear gene segments (β-fibrinogen, engrailed protein II, and myosin heavy chain II), and analyzed under maximum parsimony, maximum likelihood, and Bayesian optimality criteria to infer relationships. Chapter 1 focuses on the phylogenetic and taxonomic implications for Heteromys from the analyses of sequence data. Phylogenies also provided a framework for delimiting species boundaries within the wide-ranging Heteromys desmarestianus complex using the Wiens and Penkrot method. Several well-supported clades within this complex were recovered, including H. goldmani, H. nubicolens, and H. oresterus, as well as five groups identified as candidate species. Heteromys oasicus was not found to be genetically diagnosable from H. anomalus, and was relegated to subspecific status. I present a revised taxonomy as follows: the monotypic subgenus Xylomys is maintained (H. nelsoni); the subgenus Heteromys is divided into three species groups – anomalus (H. anomalus [including H. oasicus], H. australis, and H. teleus), desmarestianus (H. desmarestianus, H. goldmani, H. nubicolens, H. oresterus, and the five candidate species), and gaumeri (H. gaumeri). Chapter 2 describes phylogenetic inferences made from analyses of heteromyine taxa, genera Heteromys and Liomys. Many studies have recovered Liomys as paraphyletic relative to Heteromys, and the goal of this chapter was to address this taxonomic problem. The Liomys pictus species group (L. irroratus, L. pictus, and L. spectabilis) was recovered as sister to Heteromys rather than to the L. salvini group (L. adspersus and L. salvini). I recommend a revised taxonomy for the subfamily as follows: the genus Heteromys is retained as delineated in Chapter 1; the genus Liomys is reduced in scope to include only L. irroratus, L. pictus, and L. spectabilis; the subgeneric name Schaeferia is elevated to generic rank and includes S. adspersus and S. salvini. This classification better reflects the phyletic diversity within the subfamily Heteromyinae, and requires fewer name changes; thus providing nomenclatural stability.

Urinary bladder cancer is a heterogeneous disease appearing in different forms, e.g. non-muscle invasive and muscle invasive. For all variants, the expression of proteins is interesting to analyze for diagnostic, predictive, prognostic and drug targeting purposes, since it reflects the altered gene expression causing the cancer. Since urothelial cells of the bladder are in direct contact with urine it is likely that this body fluid contains cancer-related proteins. In Paper I, unbiased analysis of proteins in urine from urinary bladder cancer patients and controls, using label-free quantification by mass spectrometry, was applied and four interesting proteins APOE, FGB, LRG and SERPINA1 were selected and further analyzed with western and dot blot. In Paper II, two more proteins, POLR1E and TOP2A, were validated as relevant proteins in bladder cancer urine. In Paper III and IV, the proteins GAL1 and STMN1 were investigated for their prognostic and therapeutic target potential in bladder cancer. In Paper II, III and IV, the expression of seven of the proteins were analyzed on tissue microarrays representing tumour tissue from 360 patients with different tumour stages. For the proteins identified by the urine screening approach, their protein expressions were confirmed in bladder cancer tissue. The expression level in tissue of five of the proteins, APOE, FGB, POLR1E (Paper II), GAL1 (Paper III) and STMN1 (Paper IV), increased with tumour stage, showing diagnostic relevance and three of the proteins, SERPINA1 (Paper II), STMN1 (Paper IV) and GAL1 (Paper III) had prognostic potential in urinary bladder cancer. In addition, GAL1 and STMN1 were demonstrated to be highly expressed in metastatic disease and inhibition of STMN1 reduced cell growth (Paper III and IV), indicating that these proteins are promising drug targets in urinary bladder cancer. In conclusion, the approach of this thesis has generated several candidate protein biomarkers in urine and tissue, validated with independent methods, which have the potential to improve the care for bladder cancer patients.