<p>Lead-tin telluride alloy, Pb1-xSnxTe, is a narrow band gap group IV–VI semiconductor with NaCl-like crystalline structure. This material has interesting electronic properties, which makes it suitable for designing infrared photo detectors, diode lasers, and thermo-photovoltaic energy converters. In this project, we used spectroscopic ellipsometry in the spectral range of 0.74–6.5 eV to probe the linear optical response of Pb1-xSnxTe alloys in terms of the complex dielectric function. A strong optical response in the range of 0.7-2.0 eV arising from optical absorption was found. We studied eleven different samples of Pb1-xSnxTe of p-type origin with x values in the range (0 ≤ x ≤ 1). They were prepared by means of molecular beam epitaxy (MBE) on BaF2 substrates with 15mm2 area.</p>

Cancer has been one of main causes of human deaths for many years. Early detection of cancer is essential to provide definitive treatment. Among many cancer treatment methods, nanoparticle-mediated photothermal therapy is considered as one of the promising cancer treatment methods because of its non-invasiveness and cancer-specific therapy. Ultrasound and photoacoustic imaging can be utilized for both cancer detection and photothermal therapy guidance. Ultrasound elasticity imaging can detect cancer using tissue elastic properties. Once cancer is diagnosed, spectroscopic photoacoustic imaging can be used to monitor nanoparticle delivery before photothermal therapy. When nanoparticles are well accumulated at the tumor, ultrasound and photoacoustic-based thermal imaging can be utilized for estimating temperature distribution during photothermal therapy to guide therapeutic procedure. In this dissertation, ultrasound beamforming, elasticity imaging, and spectroscopic photoacoustic imaging methods were developed to improve cancer detection and therapy guidance. Firstly, a display pixel based synthetic aperture focusing method was developed to fundamentally improve ultrasound image qualities. Secondly, an autocorrelation based sub-pixel displacement estimation method was developed to enhance signal-to-noise ratio of elasticity images. The developed elasticity imaging method was utilized to clinically evaluate the feasibility of using ultrasound elasticity imaging for prostate cancer detection. Lastly, a minimum mean square error based spectral separation method was developed to robustly utilize spectroscopic photoacoustic imaging. The developed spectroscopic photoacoustic imaging method was utilized to demonstrate ultrasound and photoacoustic image-guided photothermal cancer therapy using in-vivo tumor-bearing mouse models. The results of these studies suggest that ultrasound and photoacoustic imaging can assist both cancer detection and therapy guidance. / text

Extensive photometric and spectroscopic observations have been obtained for the binary HS1136+6646, a newly formed post-common envelope binary system containing a hot ~DAO.5 primary and a highly irradiated secondary. H1136+6646 is the most extreme example yet of a class of short period systems containing a hot H-rich white dwarf with a K-M companion. An orbital period of 0.83607(3) days has been determined through the phasing of radial velocities, emission line equivalent widths, and photometric measurements spanning a range of 24 months. Radial velocity measurements yield an amplitude of K_WD = 69(2) km s^-1 for the white dwarf and K_K7V = 115 +/- 1 km s^-1 for the secondary star. Photometric measurements revealed a low amplitude modulation with a period of 234 minutes, associated with the rotation of the white dwarf. The white dwarf is estimated to have an effective temperature and gravity of ~100,000 K and log g~8.29 respectively, indicating the binary system is the second earliest post-CE objects known, having an age around 6.4x10^5 years. Indications are that the secondary star is overly luminous for its mass.I also present FUSE observations of the magnetic cataclysmic variable V405 Aurigae. Together with four other DQ Her type binaries, V405 Aur forms a small subclass of intermediate polars which are likely to evolve into low magnetic field strength polars. The FUSE spectrum exhibits broad O VI and C III emission-lines as well as a narrow O VI emission-line component which likely forms near the white dwarf surface in an optically thin gas. Radial velocity measurements restrict any orbital modulation to a very low amplitude (K_WD = 2.5(0.5) km s^-1) indicating that the binary system is at low inclination.Recent photometric and spectroscopic observations have revealed J0644+3344 to be a bright, deeply eclipsing cataclysmic variable binary with a 6.46488(24) hour period. Although the nature of the hot component is not presently clear, J0644+3344 is one of the brightest eclipsing nova-like cataclysmic variable system yet. As such, the possibility exists for an unambiguous determination of the masses and temperatures of both components in future studies.

Mouse embryonic stem cells (ESCs) are known to possess an “open” global chromatin architecture characterized by dispersed chromatin fibres throughout the nucleus. This is in contrast to differentiated cell types, where chromatin generally congregates into numerous compact domains. Core transcription factors in ESCs regulate many genes involved in maintaining pluripotency and previous research has hinted a connection between these factors and chromatin organization. My hypothesis is that Nanog, one of the core transcription factors, functions in maintaining an “open” chromatin organization in mouse ESCs. In this study, the chromatin organization in ESCs expressing varying levels of Nanog was examined at the sub-micron level through electron spectroscopic imaging. An inverse correlation was identified between Nanog expression level and the chromatin fibre density in constitutive heterochromatic regions. Furthermore, global chromatin in the more differentiated epiblast stem cells became less compact upon Nanog overexpression. Altogether, these findings support the idea that Nanog plays a role in maintaining dispersed chromatin in mouse ESCs.

Mouse embryonic stem cells (ESCs) are known to possess an “open” global chromatin architecture characterized by dispersed chromatin fibres throughout the nucleus. This is in contrast to differentiated cell types, where chromatin generally congregates into numerous compact domains. Core transcription factors in ESCs regulate many genes involved in maintaining pluripotency and previous research has hinted a connection between these factors and chromatin organization. My hypothesis is that Nanog, one of the core transcription factors, functions in maintaining an “open” chromatin organization in mouse ESCs. In this study, the chromatin organization in ESCs expressing varying levels of Nanog was examined at the sub-micron level through electron spectroscopic imaging. An inverse correlation was identified between Nanog expression level and the chromatin fibre density in constitutive heterochromatic regions. Furthermore, global chromatin in the more differentiated epiblast stem cells became less compact upon Nanog overexpression. Altogether, these findings support the idea that Nanog plays a role in maintaining dispersed chromatin in mouse ESCs.

Optical Coherence Tomography (OCT) is a subsurface imaging technique with many biomedical and industrial applications. In this thesis, we describe our design and implementation of a time domain OCT system. We used this system to obtain OCT images of objects that are important in different applications. We also used an existing quadrature OCT system to obtain both real and imaginary parts of an OCT image. We introduced a new interpretation of OCT images as the 2nd derivative of the scattering potential of an object. To obtain this scattering potential from its 2nd derivative, we implemented a method of definite integration in the spectral-domain. The obtained scattering potential was used to separate the scattering profile from the absorption profile of an object. We applied this new spectroscopic imaging method to quadrature OCT images of different objects.

R Coronae Borealis (RCB) stars belong to a rare class of variable stars characterized by sudden and unpredictable declines, which are believed to be caused by dust cloud obscuration. In spite of the fact that these stars are so rare (only about 40 are known in our Galaxy), there are many reasons for investigating them. The unusual variability and peculiar chemical composition make them unique among all known types of variable stars. Their evolution and the nature of their unpredictable minima are still not entirely understood. Very few observations of RCB stars during the decline phase exist. Only three RCB stars (R CrB, RY Sgr and V854 Cen) have been studied in detail and only a few declines have been completely covered by observations. This thesis investigates the spectroscopic and photometric characteristics of RCB variables during their decline phases. A programme of photometric and spectroscopic observations of nine RCB and three HdC stars has been undertaken at Mt John University Observatory (MJUO) over a period of two and a half years. The programme includes some typical examples of RCB stars (Teff ~ 7000 K), as well as some cool ones (Teff ~ 5000 K). One of the most unusual of all RCB stars, V854 Cen, is also included. The photometric observations, as part of the long-term monitoring of RCB stars at MJUO, have provided the UBVRIphotometry and have served as a decline indicator. Complex colour changes during the declines were monitored and compared with the spectroscopy. The photometry during the recovery phases of the nine RCB stars in the last 12 years was used for studying the extinction properties of the gas obscuring the photosphere. An analysis of 26 different declines shows that the material causing the declines has extinction properties similar to those of the interstellar medium. The medium and high-resolution spectroscopy has been obtained for six declines of different programme stars using the 1-m telescope at MJUO. Although the duration and depth of the declines are very different, they all show similar photometric and spectroscopic characteristics. The results have been compared with other observations and used to examine a simple line-region model (E1/E2/BL), which attempts to describe the evolution and origin of emission lines during a decline. In general, the evolution of various emission lines observed in this work is consistent with their classification into these three groups. However, some characteristics of the emission lines indicate a different origin from that suggested by the model. A very rich emission line spectrum was monitored during the 1998 decline of V854 Cen, while only the most prominent lines were observed in the other stars. Short-lived high-excitation lines from the initial decline phase, such as CI and 01, were classified as Ei. They show a characteristic, shock-induced red shift indicating the photospheric origin. Lines classified as E2 are mainly from the low-excitation ions and neutral atoms. All lines from this group appear at the very beginning of the decline and are visible through to the late recovery phase, slightly blue-shifted relative to the stellar velocity. The lines of the low-excitation ions exhibit a complex structure with a strong central and two weaker components, one on each side. Their absolute flux evolution has been compared with the changes in the stellar continuum flux. The behaviour of these lines indicates that they are not affected by the dust cloud in the same way as the photospheric continuum. Assuming that the dust cloud is formed at about 2R* and taking into account the acceleration obtained from the analysis of the high-velocity Nal D absorption lines, the position of the E2 line emitting region was estimated to be about 3R* - 5R*. The third group (BL) consists of broad emission lines, which are a typical feature of all observed declines. The most prominent broad lines present in all RCB stars belong to the Nal D doublet. The observations demonstrate that these lines are the strongest in V854 Cen, due to the significant amount of material produced by its frequent declines. In contrast to the E2 lines, whose fluxes have been found to decrease during the decline, the absolute flux of the broad lines stays constant throughout the whole decline phase. This is consistent with the idea that the broad emission is a permanent feature, whose visibility depends only on the photospheric brightness. Various Nal D components (sharp and broad emission and high-velocity absorption) have been analysed in a number of RCB declines and presented in this thesis. The high-velocity blue-shifted Nal D absorption demonstrates similar velocities (between -230 kms-1 and -400 kms-1), structure and behaviour in the different declines. The observations from the 1998 decline of V854 Cen clearly show that the high-velocity absorption lines can also appear during the initial decline phase. This suggests that they can be associated with the clouds formed in some previous declines, as well as with the current one. The spectroscopic observations of the 1998 decline of V854 Cen obtained in this thesis represent the first almost complete coverage of a decline of this star.

abstract: Magnetic resonance spectroscopic imaging (MRSI) is a valuable technique for assessing the in vivo spatial profiles of metabolites like N-acetylaspartate (NAA), creatine, choline, and lactate. Changes in metabolite concentrations can help identify tissue heterogeneity, providing prognostic and diagnostic information to the clinician. The increased uptake of glucose by solid tumors as compared to normal tissues and its conversion to lactate can be exploited for tumor diagnostics, anti-cancer therapy, and in the detection of metastasis. Lactate levels in cancer cells are suggestive of altered metabolism, tumor recurrence, and poor outcome. A dedicated technique like MRSI could contribute to an improved assessment of metabolic abnormalities in the clinical setting, and introduce the possibility of employing non-invasive lactate imaging as a powerful prognostic marker. However, the long acquisition time in MRSI is a deterrent to its inclusion in clinical protocols due to associated costs, patient discomfort (especially in pediatric patients under anesthesia), and higher susceptibility to motion artifacts. Acceleration strategies like compressed sensing (CS) permit faithful reconstructions even when the k-space is undersampled well below the Nyquist limit. CS is apt for MRSI as spectroscopic data are inherently sparse in multiple dimensions of space and frequency in an appropriate transform domain, for e.g. the wavelet domain. The objective of this research was three-fold: firstly on the preclinical front, to prospectively speed-up spectrally-edited MRSI using CS for rapid mapping of lactate and capture associated changes in response to therapy. Secondly, to retrospectively evaluate CS-MRSI in pediatric patients scanned for various brain-related concerns. Thirdly, to implement prospective CS-MRSI acquisitions on a clinical magnetic resonance imaging (MRI) scanner for fast spectroscopic imaging studies. Both phantom and in vivo results demonstrated a reduction in the scan time by up to 80%, with the accelerated CS-MRSI reconstructions maintaining high spectral fidelity and statistically insignificant errors as compared to the fully sampled reference dataset. Optimization of CS parameters involved identifying an optimal sampling mask for CS-MRSI at each acceleration factor. It is envisioned that time-efficient MRSI realized with optimized CS acceleration would facilitate the clinical acceptance of routine MRSI exams for a quantitative mapping of important biomarkers. / Dissertation/Thesis / Doctoral Dissertation Bioengineering 2016

A hemoglobina (Hb) do anelídeo Glossoscolex paulistus é uma Hb extracelular gigante. Esta é constituída por quatro cadeias polipeptídicas a, b, c e d contendo o heme. As cadeias a, b e c formam um trímero mantido por ligações dissulfeto e a cadeia d é um monômero. Neste trabalho, as técnicas espectroscópicas de absorção ótica no UV-Vís, fluorescência e dicroísmo circular foram utilizadas para monitorar as mudanças produzidas na estrutura do monômero d na forma oxi da hemoglobina extracelular gigante de Glossoscolex paulistus (HbGp) em pH 7,0 e 9,0 devido à interação com surfactantes iônicos, dodecil sulfato de sódio (SDS), cloreto de cetiltrimetilamônio (CTAC) e neutro, polioxietileno lauril éter (BRIJ - 35). A interação entre surfactantes e proteínas globulares tem sido estudada através de uma variedade de técnicas espectroscópicas visando à obtenção de informações relevantes com respeito à relação estrutura-atividade das proteínas. Os resultados de fluorescência mostraram que na presença dos surfactantes, há um aumento do rendimento quântico, sendo que o maior aumento é verificado na interação com o surfactante catiônico CTAC, sugerindo que a proteína apresenta uma quantidade maior de sítios específicos carregados negativamente, como os resíduos aniônicos, glutamil e aspartil. Na interação do monômero d da HbGp com CTAC ocorreu a formação de espécie pentacoordenada em ambos os pHs. Para o sistema monômero da HbGp-SDS em pH 7,0 e 9,0, foi observada a oxidação do monômero d, caracterizada pela formação da espécie hemicromo. A interação do monômero d em pH 7,0 e 9,0 com CTAC, analisada pelos espectros de dicroísmo circular, indicaram uma perda não muito significativa da estrutura secundária. No entanto, para os surfactantes SDS e BRIJ-35 foi possível constatar uma perda menos acentuada em relação ao CTAC. / The annelid hemoglobin (Hb) of the Glossoscolex paulistus is a giant extracellular hemoglobin (Hb). It is constituted by four polypeptide a, b, c and d chains containing the heme. The chains a, b and c form a trimer maintained by disulfide bond and the d chain is a monomer. In this work, the spectroscopic techniques of UV-Vís optical absorption, fluorescence and circular dichroism were used to monitor the changes induced by ionic detergents sodium dodecyl sulphate (SDS), cetyltrimethylammonium chloride (CTAC) and neutral, ether lauryl polioxitelene (BRIJ-35) in the structure of the d monomer in the oxi form of the giant extracellular hemoglobin of Glossoscolex paulistus (HbGp) in pH 7.0 and 9.0. The interaction between surfactants and globular proteins has been studied through a range of spectroscopic techniques targeting the obtaining of prominent information with regard to the relation structure-activity of the proteins. The fluorescence results showed that in the presence of the surfactants a quantum yield increases, and the CTAC promoted the more significant effect, suggesting that the protein presents a larger quantity of specific negative sites, as the anionic residues, glutamil and aspartil. In the interaction of d monomer of the HbGp with CTAC occurred the formation of pentacoordinated species in both pHs. For system monomer of HbGp-SDS at pH 7.0 and 9.0, was observed by oxidation of d monomer, characterized by the formation of the species hemichrome. The interaction of d monomer at pH 7.0 and 9.0 with CTAC, analyzed by circular dichroism spectra, indicates the loss of secondary structure. However, for SDS and BRIJ-35 surfactants it is possible to detect the lower loss of secondary structure in relation to CTAC.

O presente estudo avaliou a composição química da dentina radicular de dentes submetidos à radioterapia por meio de Espectroscopia Raman Confocal (ERC). Vinte pré-molares inferiores humanos homólogos foram selecionados e distribuídos em dois grupos (n=10) de acordo com a irradiação: não irradiados e irradiados, submetidos à radioterapia fraccionada com raios-X de 6 MV. Os dentes foram seccionados e submetidos à análise da composição química da dentina radicular submetida à radioterapia por meio de ERC, em relação aos picos de fosfato, carbonato e amidas I, II e III. Foi utilizada objetiva de 40x (Olympus), com luz de comprimento de onda de 785 nm, compreendendo a faixa espectral de 400 - 1800 cm-1, na região de baixa frequência, com resolução espacial de 2 &micro;m. Para a geração do espectro, a potência do laser utilizada foi de 21 mW e o tempo de exposição de 5 segundos. A intensidade dos picos fosfato - PO43- (590 cm-1) e carbonato - CO32- (1070 cm-1) no ERC são proporcionais à quantidade de conteúdo inorgânico, enquanto que a amida I (1670 cm-1), II (1453 cm-1) e III (1267 cm-1) são proporcionais ao conteúdo orgânico (colágeno). Os dados obtidos foram submetidos à análise estatística (Teste T, P<0,05) para amostras independentes, avaliando-se a influência da radioterapia nos valores de fosfato, carbonato e amidas I, II e III em diferentes regiões radiculares. Em região de dentina radicular intracanal, o grupo irradiado (1,23&plusmn;0,06) apresentou menores valores de fosfato quando comparado ao grupo não irradiado (1,40&plusmn;0,18) (P<0,05). Em relação ao carbonato, foi observado que os dentes irradiados (1,56&plusmn;0,06) apresentaram menores valores quando comparados ao grupo não irradiado (1,42&plusmn;0,10) (P<0,05). Para os picos de amida, não foi observada diferença estatística entre os grupos em amida I (P=0,295) e amida II (P=0,792). No entanto, o tratamento radioterápico reduziu significativamente os valores de amida III do grupo irradiado (1,05&plusmn;0,19) em comparação ao grupo não irradiado (1,28&plusmn;0,24). Quando avaliada a região da dentina radicular média, o grupo irradiado (1,30&plusmn;0,12) apresentou menores valores de fosfato quando comparado ao grupo não irradiado (1,48&plusmn;0,22) (P<0,05); e em relação aos valores de carbonato (P=0,859), amida I (P=0,785), amida II (P=0,771) e amida III (P=0,338) não foi observada diferença estatística entre eles. Na análise em cemento, não houve diferenças estatísticas entre os grupos irradiado e não irradiado para os valores de fosfato (P=0,448), carbonato (P=0,575) e amida I (P=0,225), amida II (P=0,437) e amida III (P=0,187). Dessa forma, pode-se concluir que a radioterapia promoveu alterações nos picos de amida III, indicando modificação estrutural do colágeno. / The present study was to evaluate the root dentin chemical composition of teeth submitted to radiotherapy by Confocal Raman Spectroscopy (CRS). Twenty inferior human homologues premolars were selected and divided in two groups (n = 10) according to the irradiation protocol: non Irradiated and irradiated, submitted to fractional X-ray radiotherapy of 6 MV. The teeth were sectioned and submitted to the analysis of the chemical composition of radicular dentin submitted to radiotherapy by CRS, evaluating the phosphate, carbonate and amides I, II and III peaks. A 40x objective (Olympus) was used, generating a light with a 785 nm wavelength, comprising the spectral range of 400-1800 cm-1 in the low frequency region with spatial resolution of 2 &micro;m. For the spectrum generating the laser power used was 21 mW and the exposure time was 5 seconds. The intensity of the phosphate - PO43- (590 cm-1) and carbonate - CO32- (1070 cm-1) peaks in the CRS are proportional to the amount of inorganic content while the amide I (1670 cm-1), II (1453 cm-1) and III (1267 cm-1) are proportional to organic content (collagen). The data were submitted to statistical analysis (Test T, P<0.05) for independent samples, evaluating the influence of radiotherapy on the phosphate, carbonate and amide I, II and III values in different root regions. In the intracanal dentin root region, the irradiated group (1.23 ± 0.06) had lower phosphate values when compared to the non-irradiated group (1.40 ± 0.18) (P<0.05). In relation to the carbonate, it was observed that the irradiated teeth (1.56 + 0.06) had lower values than the non-irradiated group (1.42 + 0.10) (P<0.05). The amide peaks has no statistical difference observed between the groups in relation to the amide I (P=0,295) and amide II (P=0,792). However, the radiotherapeutic treatment significantly reduced the amide III values of the irradiated group (1.05 + 0.19) compared to the non-irradiated group (1.28 + 0.24). When the middle radicular dentin region was evaluated, the irradiated group (1.30 ± 0.12) had lower phosphate values when compared to the non-irradiated group (1.48 ± 0.22) (P<0.05); and in relation to the carbonate (P=0.859), amide I (P=0.785), amide II (P=0,771) and amide III (P=0,338) peaks no statistical difference was showed between irradiated and non-irradiated teeth. In the cement analysis, there was no statistical difference between the irradiated and non-irradiated groups for the phosphate (p = 0.448), carbonate (P=0.575), amide I P=0.225), amide II (P=0,437) and amide III (P=0,187) values. In conclusion, the radiotherapy was able to promote alterations in the amide III, changing the collagen structure.