Erros de alinhamento em sistemas ópticos não criam novas aberrações, mas alteram a dependência com o campo das aberrações já conhecidas. Neste trabalho, a sensibilidade teórica ao alinhamento, de sistemas ópticos reflexivos compostos por dois elementos, foi avaliada em função das constantes cônicas dos espelhos. Dentre as diferentes configurações consideradas nesta análise, uma específica apresenta menor sensibilidade à descentralização do espelho secundário. A utilização da teoria de aberração de onda aplicável a sistemas plano-simétricos revelou que a escolha apropriada da constante cônica do espelho secundário faz com que coma uniforme de terceira ordem seja compensado quando esse elemento encontra-se descentralizado, fazendo com que esse sistema seja livre da aberração mais importante causada a ele por desalinhamentos, tornando-o menos sensível. Este trabalho apresenta uma metodologia de alinhamento baseada na análise da frente de onda transmitida por sistemas ópticos, que utiliza redes neurais artificiais para a estimativa dos erros de alinhamento. A frente de onda transmitida por um sistema óptico carrega informações das aberrações desse sistema, que podem ser descritas em termos dos polinômios de Zernike. Esses polinômios podem ser usados para a análise dos efeitos de erros de alinhamento nas aberrações do sistema. Redes neurais artificiais são empregadas na análise dos coeficientes dos polinômios de Zernike visando avaliar o tipo de desalinhamento e a sua magnitude. As estimativas teóricas dos desalinhamentos tanto em sistemas reflexivos como em sistemas refrativos são satisfatórias quando o sistema é considerado perfeito, ou seja, as superfícies ópticas de seus elementos não apresentam erros de forma e não há ruído nos dados avaliados. Na presença de defeitos de fabricação ocorre degradação no desempenho do estimador. Além de descentralização e inclinação, redes neurais artificiais são capazes de fornecer uma estimativa de erros de posicionamento axial dos elementos do sistema. Com base nos estudos realizados, acredita-se que redes neurais artificiais constituem uma alternativa promissora no alinhamento de sistemas ópticos complexos. / Although misalignments in optical systems do not generate new aberration forms, they change the field-dependence of the known ones. In this research, the sensitivity of two-mirror optical systems due to misalignments is evaluated in function of the conic constants of the mirrors. Among the different configurations considered in this study, a specific one has shown low sensitivity due to decenter misalignments. The application of the wave aberration theory for plane-symmetric optical systems has revealed that the proper choice of the secondary mirror conic constant allows third-order uniform coma to be compensated, leading to a less sensitive system, free from the most important misalignment-induced aberration. This thesis also presents an alignment methodology based on the analysis of the transmitted wavefront utilizing artificial neural networks to estimate alignment errors in the components of the system. The transmitted wavefront carries information about the aberrations in the optical system, which can be described in terms of Zernike polynomials. Such polynomials are used for the analysis of the effects of misalignments on the aberrations of the system. Artificial neural networks are employed in the analysis of the coefficients of Zernike polynomials and used to evaluate both type and magnitude of the misalignments. Theoretical misalignments estimated in reflexive and refractive optical systems are satisfactory for perfect systems, i.e., systems with no surface errors, and noiseless data. When surface imperfections are considered, the performance of the estimator is reduced. Besides decenter and tilt misalignments, artificial neural networks can estimate axial positioning errors of the elements in the system, therefore they are believed to be a promising alternative for the alignment of complex optical systems.

目前廣泛應用于胎兒醫學的唐氏綜合症篩查法，即結合早孕期胎兒頸項透明層的超聲檢查，及母體血清生化指標的綜合篩查法。頸項透明層是指在早孕期利用超聲檢測到的胎兒頸后的皮下積水，其作為預測胎兒異常的一項重要“軟指標，其臨床意義，尤其是與胎兒染色體異常及器官結構異常之間的關係，逐漸得到深入的認識，但其形成機制尚未明確。現在已知有一百餘種畸形及遺傳綜合征與胎兒頸項透明層增厚相關，但其染色體異常譜系，尤其是亞顯微的染色體異常仍有待明確。大部分頸項透明層增厚但核型正常的胎兒預後良好，但約3-10%的這部分胎兒會伴有畸形或出生后的神經智力發育缺陷。而傳統核型分析無法檢測到亞顯微的染色體異常，從而無法判斷這部分核型正常卻伴有缺陷的胎兒是否因為這類染色體異常而致病。 / 微陣列比較基因組雜交芯片作為檢測兒童發育遲緩者及器官結構異常原因的重要手段已廣泛應用于臨床。在染色體核型正常的胎兒中，若伴有器官結構異常的胎兒，5-12%被檢出與該畸形相關的微缺失及微重複；若僅伴有孕婦高齡或唐氏篩查高危，則微缺失及微重複檢出率約1%。 / 該課題旨在研究頸項透明層增厚但核型正常的胎兒中，染色體拷貝數變異發生的頻率及頻譜；評估微陣列比較基因組雜交芯片在協助臨床判斷胎兒預後中的作用。因此，我們開展該多中心隊列研究，通過納入449例頸項透明層厚度≧3.5 mm但正常核型胎兒的，檢測其染色體拷貝數變異，監測并記錄其圍產、產後及新生兒期情況。微陣列比較基因組雜交芯片總共檢出2.8%的異常拷貝數變異，其大小範圍為0.1 kb至18Mb。在伴有器官結構異常的胎兒組中，異常拷貝數變異檢出率達7.8%。對於頸項透明層厚度≧4.0 mm的胎兒，異常拷貝數變異檢出率可達7.3%。 / 對於頸項透明層增厚的胎兒，致病拷貝數變異暫未發現特定的頻譜。但，該研究中發現重複的致病拷貝數變異，如22號染色體長臂1區1帶的微重複或微缺失，2號染色體長臂2區2帶的微缺失。未在3號、7號、12號、13號、18號、20號、21號或Y染色體上發現與胎兒頸項透明層增厚相關的致病拷貝數變異。 / 頸項透明層增厚的胎兒79.3%預後良好；若經微陣列比較基因組雜交芯片未檢出致病拷貝數變異，則81.2%預後良好。如果僅頸項透明層增厚不伴有結構異常的胎兒，經微陣列比較基因組雜交芯片未檢出致病拷貝數變異，則93.5%預後良好。 / 綜上所述，微陣列比較基因組雜交芯片顯著提高了致病拷貝數變異的檢出率。可考慮將微陣列比較基因組雜交芯片作為頸項透明層厚度≧4.0 mm的胎兒染色體異常檢查的首要方法。對於僅頸項透明層增厚不伴有結構異常的胎兒，且經微陣列比較基因組雜交芯片未檢出致病拷貝數變異，絶大部分預後良好。對於頸項透明層增厚的胎兒，致病拷貝數變異暫未發現特定的頻譜，但發現重複出現的致病拷貝數變異。通過初步的基因本體分析及基因通路分析，神經嵴細胞的分化遷徙功能異常可作為今後研究頸項透明層增厚的病理生理機制的方向。 / Measurement of nuchal translucency (NT) has been recognized as a sensitive marker for fetal chromosomal disorders for more than a decade, and is presently used as a routine first-trimester screening test. Although over 100 abnormalities and genetic syndromes have been reported to be associated with increased NT, these associations have not been fully explored and the relevant spectrum of associated submicroscopic chromosomal abnormalities has not been sufficiently investigated. The majority of euploid fetuses with increased NT have a good outcome, but around 3-10% of fetuses present with structural or neurodevelopmental abnormalities postnatally. A range of genetic syndromes has been reported, many of which are linked to submicroscopic chromosomal abnormalities that are typically missed by conventional karyotyping. / Microarray-based comparative genomic hybridization (arrayCGH) has been applied as the first-tier diagnostic tool for the evaluation of developmental delay and structural malformations in children. In fetuses with a normal karyotype, microarray analysis revealed clinically relevant deletions or duplications in 5-12% with a structural anomaly and in about 1% of those whose indications were advanced maternal age or positive screening results. / The objectives of this study were to delineate the frequency and spectrum of pathogenic chromosome copy number variants (CNVs) among fetuses with increased NT and normal karyotype; to evaluate the role of arrayCGH to predict the prognosis of the high NT fetuses; to explore the genotype-phenotype correlations of increased NT. Therefore, a multi-centre cohort of 449 fetuses with NT ≧3.5 mm and normal karyotype were further investigated by arrayCGH. Antenatal surveillance, pregnancy outcome and paediatric follow up were documented. ArrayCGH detected abnormal CNVs in 2.8% (14 of 449) of the fetuses with high NT; the size of CNVs ranged from 0.1 kb to 18Mb. Among fetuses with major congenital abnormalities the incidence of abnormal CNV reached 7.8% (4 of 51). By adjusting the NT to ≧4.0 mm as the referral indication, 7.3% (14 of 192) of the fetuses would have abnormal arrayCGH results. The spectrum of pathogenic CNVs found associated with increased NT was diverse. However, there were recurrent ones such as the deletions or duplications at chromosomal region 22q11, and deletions in ZEB2. There was no pathogenic CNV related with increased NT found in chromosomes 3, 7, 12, 13, 18, 20, 21, or Y. The total normal outcome rate of euploid fetuses with an increased NT was 79.3%; for fetuses with normal arrayCGH results 81.2% had a normal outcome. In fetuses with isolated increased NT, normal arrayCGH results predict a favorable prognosis of 93.5%. / In conclusion, arrayCGH significantly increased the diagnostic yield of pathogenic CNVs. In clinical practice arrayCGH may be considered as the first tier investigation in fetuses with an increased NT more than 4.0 mm. In cases with an isolated increased NT with normal arrayCGH results the pregnancy outcome is likely to be favorable. The spectrum of abnormal CNVs found by arrayCGH is diverse but there are recurrent cases such as del/dup 22q11 and del ZEB2. Our preliminary gene ontology and pathway analysis showed that gene pathways related to neural crest cells may be considered as a future study for physiopathologic mechanisms of NT. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Huang, Jin. / Thesis (Ph.D.) Chinese University of Hong Kong, 2014. / Includes bibliographical references (leaves 106-120). / Abstracts also in Chinese.

O 153Sm-EDTMP é um radiofármaco utilizado em medicina nuclear com resultados promissores no alívio da dor metastática. No entanto, pouco se sabe sobre os efeitos do 153Sm-EDTMP em nível celular. O presente trabalho foi conduzido com o intuito de avaliar os efeitos citogenéticos do 153Sm-EDTMP em linfócitos periféricos de pacientes com metástases ósseas (com e sem radio e/ou quimioterapias anteriores) pela da técnica de detecção de aberrações cromossômicas, tanto in vivo como in vitro. Para tanto, as amostras sangüíneas foram coletadas antes e 1 hora após a administração endovenosa do 153Sm- EDTMP (atividade média de 42,53 + 5,31 MBq/kg de peso corpóreo), levando-se em consideração o rápido clearance sangüíneo. Os principais tipos de aberrações cromossômicas estruturais encontrados foram os gaps e quebras, fragmentos acêntricos, anéis cêntricos, double minutes e dicêntricos. A análise estatística mostrou que o único grupo de pacientes que apresentou uma diferença significativa na freqüência de aberrações cromossômicas 1 hora após o tratamento foi o que recebeu prévio tratamento radio e quimioterápico antes da terapia com 153Sm-EDTMP. Quanto a averiguação do número modal de cromossomos e da cinética do ciclo celular, a análise estatística mostrou que não houve diferença significativa entre os grupos analisados, sugerindo que o tratamento com 153Sm-EDTMP não influenciou nesses parâmetros. A molécula carreadora, EDTMP, não teve qualquer influência na indução de aberrações cromossômicas. Em relação aos ensaios in vitro, os dados obtidos de linfócitos periféricos submetidos às diferentes concentrações radioativas de 153Sm-EDTMP (0,046 – 1,110 MBq/mL) de doadores sadios e de pacientes sem prévio tratamento se ajustaram melhor ao modelo de regressão linear (Y=A+BX). O dano cromossômico induzido pelo 153Sm-EDTMP observado in vitro foi cerca de 2 vezes maior do que o encontrado in vivo para o grupo de pacientes sem prévio tratamento. Os dados obtidos mostraram que a terapia com 153Sm-EDTMP induziu uma pequena quantidade de danos citogenéticos em linfócitos periféricos de pacientes 1 hora após sua administração, embora, teoricamente, um efeito estocástico a longo prazo não possa ser descartado. / The 153Sm-EDTMP is a radiopharmaceutical used in nuclear medicine with promising results for the relief of metastatic pain. Therefore, there are few knowledge about the effects of 153Sm-EDTMP at cellular level. The present study was conducted with the aim of evaluating the cytogenetic effects of 153Sm-EDTMP in peripheral lymphocytes from patients with bone metastasis (with and without previous radio and/or chemotherapy) by the chromosome aberration technique, either in vivo or in vitro. For that, the blood samples were collected before and one hour after the endovenous administrations of 153Sm-EDTMP (mean activity of 42.53 + 5.31 MBq/kg body weight), taking into account the rapid blood clearance. The principal types of structural chromosome aberrations found gaps and breaks, acentric fragments centric rings, double minutes and dicentrics. The statistical analysis showed that the group submitted to previous radio and chemotherapy before153Sm-EDTMP administration showed significant difference in chromosome aberrations frequency one hour after the treatment. The analysis of the chromosome modal number and the kinetics of cellular cycle showed no statistical difference among the groups, suggesting that the treatment with 153Sm-EDTMP, did not influence these parameters. The carrier molecule, EDTMP, did not influence the induction of chromosome aberration. In relation to the in vitro assays, the obtained data of peripheral lymphocytes of healthy donors and patients with no previous treatment exposed to different radioactive concentration of 153Sm-EDTMP (0.046 – 1.110 MBq/mL) were better adjusted by linear regression model (Y=A+BX). The chromosome damage induced by 153Sm-EDTMP observed in vitro was about 2 fold higher than that found in vivo for the group of patients with no previous treatment. The obtained data showed that the therapy with 153Sm- EDTMP induced a few quantity of cytogenetic damages in peripheral lymphocytes one hour after its administration in patients, although, theoretically, a long term stochastic effect cannot be disregarded.

Made available in DSpace on 2014-06-11T19:30:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-12-17Bitstream added on 2014-06-13T20:01:10Z : No. of bitstreams: 1 ventura_bc_dr_rcla.pdf: 1747414 bytes, checksum: d6fd71edeabed9a63deeb67289ab785e (MD5) / Os azocorantes são substâncias químicas extremamente utilizadas em indústrias têxteis que podem induzir mudanças no material genético de organismos expostos, mesmo que essas alterações no DNA não se expressem de imediato. Foram avaliadas as citotoxicidade, genotoxicidade e mutagenicidade de diferentes concentrações (1, 10, 100 e 1000 mg/L – na ausência dos microorganismos – e 50 e 200 mg/L – na presença dos microorganismos) do azocorante Black Dye Commercial Product (BDCP), antes e após tratamentos de biodegradação por diversos microrganismos (1. “Pool” de bactérias heterotróficas provenientes de uma estação de tratamento biológico de efluentes, 2. Levedura Candida viswanathii, e 3. Fungo Basidiomiceto Phanerochaete chrysosporium), por meio de diferentes técnicas citogenéticas (coloração convencional, bandamento C, bandamento RON, bandamento por fluorocromos base-específicos CMA/DAPI e hibridação in situ fluorescente – FISH) aplicadas sobre o organismo teste Allium cepa. Pela técnica citogenética de coloração convencional, foi possível verificar que o corante, com e sem ação microbiana, induziu apoptose, necrose, células micronucleadas, aberrações cromossômicas e alterações nucleares. As aberrações cromossômicas e alterações nucleares foram visualizadas em todos os estágios do ciclo celular: na intérfase foram observados brotos nucleares e células poliplóides; na prófase, perdas de material genético; na metáfase, aderências cromossômicas, perdas cromossômicas, C-metáfases e poliploidias; na anáfase e telófase, multipolaridades, pontes e perdas cromossômicas. Os brotos nucleares apareceram com maior freqüência nas células submetidas aos testes do azocorante tratado com microorganismos, sendo que esse tipo de alteração deve estar associado à presença dos metabólitos do corante. As freqüências de micronúcleos... / Azo dyes are chemical substances extremely used by textile industries that may induce changes in the genetic material of exposed organisms, even if these changes in the DNA do not express themselves immediately. Cytotoxicity, genotoxicity and mutagenicity evaluations of the different azo dye (BDCP) concentrations were performed (1, 10, 100 e 1000 mg/L – without microorganisms – and 50 and 200 mg/L – with microorganisms), before and after biodegradation tests, using different microorganisms (1. Heterotrofic bacteria ”pool” proceeding from an effluent biological treatment station, 2. Candida viswanathii - Yeast, and 3. Phanerochaete chrysosporium - Basidiomicet Fungi), by means the different cytogenetical assays (conventional staining, C-banding, RON-banding, CMA/DAPI banding and fluorescent in situ fluorescent hybridization), using Allium cepa as test organism. By the conventional staining cytogenetic assay, it was possible to verify that the azo dye induced apoptosis, necrosis, micronuclei, chromosome aberrations and nuclear alterations. The chromosome aberrations and nuclear alterations were visualized in all phases of the cell cycle: in the interphase were observed nuclear buds and polyploidizated cells; in the prophase were observed genetic material losses; in the metaphase were observed chromosome adherences, chromosome losses, C-metaphases and polyploid cells; and in the anaphase and telophase were observed multipolar cells, chromosome bridges and chromosome losses. The frequencies of nuclear buds were the higher when the cells had been submitted to the azodye treated with microorganisms, suggesting that this kind of alteration must be associated to the presence of the azodye metabolites. The micronuclei and chromosome breaks frequencies... (Complete abstract click electronic access below)

O 153Sm-EDTMP é um radiofármaco utilizado em medicina nuclear com resultados promissores no alívio da dor metastática. No entanto, pouco se sabe sobre os efeitos do 153Sm-EDTMP em nível celular. O presente trabalho foi conduzido com o intuito de avaliar os efeitos citogenéticos do 153Sm-EDTMP em linfócitos periféricos de pacientes com metástases ósseas (com e sem radio e/ou quimioterapias anteriores) pela da técnica de detecção de aberrações cromossômicas, tanto in vivo como in vitro. Para tanto, as amostras sangüíneas foram coletadas antes e 1 hora após a administração endovenosa do 153Sm- EDTMP (atividade média de 42,53 + 5,31 MBq/kg de peso corpóreo), levando-se em consideração o rápido clearance sangüíneo. Os principais tipos de aberrações cromossômicas estruturais encontrados foram os gaps e quebras, fragmentos acêntricos, anéis cêntricos, double minutes e dicêntricos. A análise estatística mostrou que o único grupo de pacientes que apresentou uma diferença significativa na freqüência de aberrações cromossômicas 1 hora após o tratamento foi o que recebeu prévio tratamento radio e quimioterápico antes da terapia com 153Sm-EDTMP. Quanto a averiguação do número modal de cromossomos e da cinética do ciclo celular, a análise estatística mostrou que não houve diferença significativa entre os grupos analisados, sugerindo que o tratamento com 153Sm-EDTMP não influenciou nesses parâmetros. A molécula carreadora, EDTMP, não teve qualquer influência na indução de aberrações cromossômicas. Em relação aos ensaios in vitro, os dados obtidos de linfócitos periféricos submetidos às diferentes concentrações radioativas de 153Sm-EDTMP (0,046 – 1,110 MBq/mL) de doadores sadios e de pacientes sem prévio tratamento se ajustaram melhor ao modelo de regressão linear (Y=A+BX). O dano cromossômico induzido pelo 153Sm-EDTMP observado in vitro foi cerca de 2 vezes maior do que o encontrado in vivo para o grupo de pacientes sem prévio tratamento. Os dados obtidos mostraram que a terapia com 153Sm-EDTMP induziu uma pequena quantidade de danos citogenéticos em linfócitos periféricos de pacientes 1 hora após sua administração, embora, teoricamente, um efeito estocástico a longo prazo não possa ser descartado. / The 153Sm-EDTMP is a radiopharmaceutical used in nuclear medicine with promising results for the relief of metastatic pain. Therefore, there are few knowledge about the effects of 153Sm-EDTMP at cellular level. The present study was conducted with the aim of evaluating the cytogenetic effects of 153Sm-EDTMP in peripheral lymphocytes from patients with bone metastasis (with and without previous radio and/or chemotherapy) by the chromosome aberration technique, either in vivo or in vitro. For that, the blood samples were collected before and one hour after the endovenous administrations of 153Sm-EDTMP (mean activity of 42.53 + 5.31 MBq/kg body weight), taking into account the rapid blood clearance. The principal types of structural chromosome aberrations found gaps and breaks, acentric fragments centric rings, double minutes and dicentrics. The statistical analysis showed that the group submitted to previous radio and chemotherapy before153Sm-EDTMP administration showed significant difference in chromosome aberrations frequency one hour after the treatment. The analysis of the chromosome modal number and the kinetics of cellular cycle showed no statistical difference among the groups, suggesting that the treatment with 153Sm-EDTMP, did not influence these parameters. The carrier molecule, EDTMP, did not influence the induction of chromosome aberration. In relation to the in vitro assays, the obtained data of peripheral lymphocytes of healthy donors and patients with no previous treatment exposed to different radioactive concentration of 153Sm-EDTMP (0.046 – 1.110 MBq/mL) were better adjusted by linear regression model (Y=A+BX). The chromosome damage induced by 153Sm-EDTMP observed in vitro was about 2 fold higher than that found in vivo for the group of patients with no previous treatment. The obtained data showed that the therapy with 153Sm- EDTMP induced a few quantity of cytogenetic damages in peripheral lymphocytes one hour after its administration in patients, although, theoretically, a long term stochastic effect cannot be disregarded.

Made available in DSpace on 2016-08-19T17:47:09Z (GMT). No. of bitstreams: 1 Antonio Alberto Carvalho.pdf: 630872 bytes, checksum: 13ecf29f7245808d06388075ae78be17 (MD5) Previous issue date: 2006-06-16 / In this study the results of the evaluation cytogenetics of 694 patients with suspected of being carriers of chromosomal abnormality, seen in Sarah Network of Hospitals for Rehabilitation - San Luis Unit, in the period from December 1996 to January 2005. / Neste estudo são apresentados os resultados da avaliação citogenética de 694 pacientes, com suspeita de serem portadores de anomalia cromossômica, atendidos na Rede Sarah de Hospitais de Reabilitação - Unidade São Luís, no período de dezembro de 1996 a janeiro de 2005.

La présence de polymères flexibles de grande masse molaire modifie de manière spectaculaire les écoulements de solution même en régime dilué. Il y a un couplage fortement non linéaire entre le champ de vitesse de la solution et la conformation microscopique des chaînes de polymères. Ce couplage est le plus efficace en écoulement élongationnel. Cette thèse porte sur l'étude de ce couplage, et sur les moyens de corréler les contraintes élongationnelles macroscopiques avec l'observation de la microstructure. Le détachement d'une goutte de solutions d'ADN (un biopolymère pouvant être visualisé) en solvant visqueux est ralenti par la formation d'un filament. La dynamique d'amincissement du filament, observée avec une caméra rapide, se déroule à taux d'élongation constant. Cela permet la mesure de la viscosité élongationnelle très élevée de ces solutions. Cette mesure a lieu dans l'air et dans un fluide d'immersion suffisamment peu visqueux. Il est possible de visualiser l'ADN par microscopie de fluorescence, mais pas au sein d'un filament cylindrique entouré d'air. On immerge l'échantillon pour adapter l'indice et faire disparaitre l'interface courbe. Plusieurs méthodes de correction (notamment la réalisation d'un objectif de microscope spécifique) sont étudiées pour pallier aux très fortes aberrations optiques qui empêchent l'observation de l'ADN. De plus, les effets de la transition de déroulement et de la viscosité élongationnelle sont aussi étudiés au sein d'écoulements microfluidiques à dominante élongationnelle.

Gene activity is regulated at two separate layers. Through structural and chemical properties of DNA – the primary layer of encoding – local signatures may enable, or disable, the binding of proteins or complexes of them with regulatory potential to the DNA. At a higher level – the structural layer of encoding – gene activity is regulated through the properties of higher order DNA structure, chromatin, and chromosome organization. Cells with abnormal chromosome compaction or organization, e.g. cancer cells, may thus have perturbed regulatory activities resulting in abnormal gene activity. Hence, there is a great need to decode the transcriptional regulation encoded in both layers to further our understanding of the factors that control activity and life of a cell and, ultimately, an organism. Modern genome-wide studies with those aims rely on data-intense experiments requiring sophisticated computational and statistical methods for data handling and analyses. This thesis describes recent advances of analyzing experimental data from quantitative biological studies to decipher the structural layer of encoding in human cells. Adopting an integrative approach when possible, combining multiple sources of data, allowed us to study the influences of chromatin (Papers I and II) and chromosomal aberrations (Paper IV) on transcription. Combining chromatin data with chromosomal aberration data allowed us to identify putative driver oncogenes and tumor-suppressor genes in cancer (Paper IV). Bayesian approaches enabling the incorporation of background information in the models and the adaptability of such models to data have been very useful. Their usages yielded accurate and narrow detection of chromosomal breakpoints in cancer (Papers III and IV) and reliable positioning of nucleosomes and their dynamics during transcriptional regulation at functionally relevant regulatory elements (Paper II). Using massively parallel sequencing data, we explored the chromatin landscapes of human cells (Papers I and II) and concluded that there is a preferential and evolutionary conserved positioning at internal exons nearly unaffected by the transcriptional level. We also observed a strong association between certain histone modifications and the inclusion or exclusion of an exon in the mature gene transcript, suggesting a functional role in splicing.

B-cell chronic lymphocytic leukemia (B-CLL) is the most common leukemia among the adult population in western countries and accounts for 30-40% of all leukemias. With survival time ranging from months to decades, the clinical course of individual CLL patients is highly variable. This heterogeneity and in the end the need for means to identify the patients with less favorable disease has encouraged the search for biomarkers that can predict the prognosis. Telomeres are repetitive structures protecting the chromosomal endings and shorten at each cell division. Telomere length (TL) has been indicated as a prognostic factor both in hematological malignancies and solid tumors. In B-CLL, TL is associated with mutation status of the immunoglobulin heavy chain variable (IGHV) gene and with clinical course. In the present thesis the main aim was to evaluate TL as a biomarker in B-CLL using a quantitative PCR-based method for TL determination. In paper I, TL was shown to be a prognostic factor for stage A and stage B/C patients, whereas IGHV mutation status predicted outcome only in stage A patients. Moreover, IGHV mutated CLL cases were subdivided by TL into two groups with different prognosis, a subdivision not seen for unmutated cases. Interestingly, the IGHV-mutated group with short telomeres had en overall survival close to that of the unmutated cases. Thus, a combination of IGHV mutation status and telomere length gave an improved subclassification of CLL identifying previously unrecognized patient groups with different outcomes. TL correlates with cellular origin of B-cell malignancies in relation to the germinal center (GC). In paper II different B-cell lymphoma/leukemia subtypes were analyzed. Shortest telomeres were found in IGHV unmutated CLLs, differing significantly from IGHV mutated cases. Contrary to this, mantle cell lymphomas (MCL) demonstrated similar TL regardless of IGHV mutation status. TL differed significantly between GC-like and non-GC-like diffuse large B-cell lymphomas (DLBCL) and follicular lymphomas (FL) had shorter telomeres than GC-like DLBCL. Hairy cell leukemias, which display Ig gene intraclonal heterogeneity, had longer telomeres than FLs and non-GC-DLBCL, but shorter than GC-DLBCL. In conclusion, TL seemed not to simply correlate with GC origin. Paper III presents a B-CLL cohort assessed for TL, genomic aberrations, IGHV mutation status, CD38 and ZAP-70 expression. An inverse correlation existed between TL and IGHV homology, CD38 and ZAP-70 expression. The presence of genomic aberrations was similar among patients regardless of TL. In contrast, 13q deletion, a favorable biomarker, was more frequent in patients with long telomeres, while 11q and 17p deletions (markers of less favorable outcome) were more frequent in the subgroup with short telomeres. In paper IV a large group of mainly indolent CLL cases from a population based cohort was studied again showing an association between TL and prognosis, especially in “good” prognosis cases as defined by other biomarkers. Multivariate analysis indicated a strong connection between IGHV mutation status, lipoprotein lipase (LPL) expression and TL. A comparison of TL in diagnostic and follow up samples demonstrated a significant correlation, and also in the follow samples TL constituted a significant biomarker for survival.

Bakalauro darbą „Įstrižojo astigmatizmo kompiuterinis modeliavimas sferiniuose ir asferiniuose lęšiuose“ sudaro įvadas, 5 dėstymo skyriai, išvados ir priedai. Darbe pateikiami 50 paveikslai ir 2 lentelės, cituojami 16 literatūros šaltinių. Darbo apimtis 66 lapai. Darbe apibendrinta literatūra apie lęšių aberacijas, jų įtaką regėjimo kokybei, bei minimalizavimą asferiniais lęšiais. Taip pat pateikiami matematiniai sferinių ir asferinių lęšių modeliai, bei įstrižojo astigmatizmo analizė šiuose lęšiuose. Įvade iškeliami darbo tikslai ir uždaviniai. Pirmajame skyriuje pateikta teorinė medžiaga apie lęšių aberacijas, antrajame – apie sferinius ir asferinius lęšius. Išanalizuoti galimi asferinių lęšių paviršiai ir jų pranašumas prieš sferinius paviršius. Trečiajame skyriuje pateikiamas matematinis spindulių eigos modelis sferiniame paviršiuje. Ketvirtajame – matematinis spindulių eigos modelis asferiniame paviršiuje. Penktajame skyriuje lyginami kompiuterinių modelių pagalba gauti įstrižojo astigmatizmo apibūdinti rezultatai, tangentinėmis paklaidomis. / The bachelor’s thesis „The computer modeling of oblique astigmatism in spherical and aspherical lenses” consists of introduction, 5 chapters, conclusions and attachments. The thesis introduces 50 figures, 2 tables and refers to 16 literary sources. The volume of the work is 66 pages. The work summarizes the literature which describes the lens aberrations, its influence to quality of vision and reduction by using aspheric lenses. There is also included mathematical models of spherical and aspheric lenses, and analysis of oblique astigmatism in them. The introduction sets the aims and the goals of the study. The first chapter contains theoretic material about lens aberrations, the second – about spherical and aspheric lenses, the analysis about available surfaces of aspheric lenses and advantages of them. The third chapter contains mathematical model of light rays pathway in spherical lenses. The fourth chapter contains mathematical model of light rays pathway in aspheric lenses. The fifth chapter contains comparison of oblique astigmatism described as tangential errors in those two models.