Chronic Obstructive Pulmonary Disease (COPD) is the 3rd leading cause of death in the US, and idiopathic pulmonary fibrosis (IPF), a type of Interstitial Lung Disease (ILD), is a fast acting, irreversible disease that leads to mortality within 3-5 years. RNA-sequencing provides the opportunity to quantitatively examine the sequences of millions mRNAs, and offers the potential to gain unprecedented insights into the structure of chronic non-malignant lung disease transcriptome. By identifying changes in splicing and novel loci expression associated with disease, we may be able to gain a better understanding of their pathogenesis, identify novel disease-specific biomarkers, and find better targets for therapy. Using RNA-seq data that our group generated on 281 human lung tissue samples (47=Control, 131=COPD, 103=ILD), I initially defined the transcriptomic landscape of lung tissue by identifying which genes were expressed in each tissue sample. I used a mixture model to separate genes into reliable and not reliable expression. Next, I employed reads that overlapped splice junctions in a linear model interaction term to identify disease-specific differential splicing. I identified alternatively spliced genes between control and disease tissues and validated three (PDGFA, NUMB, SCEL) of these genes with qPCR and nanostring (a hybridization-based barcoding technique used to quantify transcripts). Finally, I implemented and improved a pipeline to perform transcriptome assembly using Cufflinks that led to the identification of 1,855 novel loci that did not overlap with UCSC, Vega, and Ensembl annotations. The loci were classified into potential coding and non-coding loci (191 and 1,664, respectively). Expression analysis revealed that there were 120 IPF-associated and 10 emphysema-associated differentially expressed (q < 0.01) novel loci. RNA-seq provides a high-resolution transcript-level view of the pulmonary transcriptome and its modification in lung disease. It has enabled a new understanding of the lung transcriptome structure because it measures not only the transcripts we know but also the ones we do not know. The approaches and improvements I have employed have identified these novel targets and make possible further downstream functional analysis that could identify better targets for therapy and lead to an even better understanding of chronic lung disease pathogenesis. / 2999-01-01T00:00:00Z

O objetivo deste estudo foi avaliar as medidas de volume e densidade pulmonar em exames de tomografia computadorizada de alta resolução (TCAR) de tórax de pacientes com esclerose sistêmica (ES), antes e após o transplante de medula óssea (TMO). As medidas foram comparadas com a avaliação funcional e resposta ao tratamento. Este foi um estudo retrospectivo observacional. A avaliação clínica e tomográfica foi realizada antes, após 6 e 18 meses do TMO, dos pacientes com ES que realizaram o procedimento entre 2011 e 2017. A análise quantitativa da TCAR foi feita utilizando programa totalmente automatizado (Yacta), capaz de obter o volume pulmonar, a densidade pulmonar média e os percentis de atenuação (P10, P40, P50, P80 e P90). Os dados clínicos, incluindo o resultado das espirometrias, foram obtidos dos prontuários eletrônicos dos pacientes. A capacidade vital forçada (CVF) aos 18 meses foi utilizada para classificar os pacientes em grupo \"melhor resposta\" (aumento >= 10% dos valores da CVF) ou \"resposta estável\" (redução, estabilidade ou aumento < 10% na CVF). Nenhum paciente apresentou redução da CVF > 10% pós-TMO. Foram incluídos 33 pacientes, com alteração tomográfica ou da função pulmonar antes da realização do TMO. O grupo \"melhor resposta\" foi composto por 15 pacientes (45,4%, 4 homens, idade média de 32,1 anos), enquanto o grupo \"resposta estável\" por 18 pacientes (54,6%, 4 homens, idade média de 37,5 anos). A análise quantitativa das TCAR não demonstrou diferença significativa entre os grupos na fase pré-TMO. No grupo \"melhor resposta\" houve redução significativa da densidade pulmonar média e dos valores dos percentis de densidade após o TMO, destacando-se os percentis 80 e 90. No grupo \"resposta estável\" não houve alteração significativa pós-TMO nos valores de volumes e densidades pulmonares. Concluímos que a análise quantitativa automática da TCAR de pacientes com ES foi capaz de identificar redução significativa da densidadepulmonar nos pacientes com melhora significativa da função pulmonar. Inferimos que, além dos volumes e densidades médias, podem ser utilizados também os percentis de densidade como parâmetro no acompanhamento da doença intersticial. Esta ferramenta pode representar um biomarcador na avaliação de tratamento da doença intersticial pulmonar na ES, complementando as provas de função pulmonar. / The purpose of this study was to evaluate pulmonary volume and density measurements in high resolution computed tomography (HRCT) scans of patients with systemic sclerosis (SSc) before and after bone marrow transplantation (BMT). Measurements were compared with functional assessment and response to treatment. This was a retrospective observational study. Clinical and tomographic evaluation of patients was performed before, after 6 and 18 months of BMT, for patients submitted to the procedure between 2011 and 2017. The quantitative analysis of HRCT scans was performed using a fully automated program (Yacta), capable of obtaining lung volume, density and attenuation percentiles (P10, P40, P50, P80 and P90). Clinical data, including the results of spirometry, were obtained from patients\' electronic records. Forced vital capacity (FVC) at 18 months was used to classify patients into \"best response\" group (>= 10% increase in FVC values) or \"stable response\" (reduction, stability or FVC increase < 10%). No patient had FVC reduction > 10% after BMT. Thirty-three patients were included, with tomographic or pulmonary function alterations before the BMT. The \"best response\" group consisted of 15 patients (45.4%, 4 men, mean age 32.1 years), while the \"stable response\" group comprised 18 patients (54.6%, 4 men, mean age of 37.5 years). Quantitative analysis of HRCT did not show a significant difference between the groups in the pre-BMT evaluation. In the \"best response\" group there was a significant reduction in mean lung density and density percentile values after BMT, with emphasis on the 80th and 90th percentiles. In the \"stable response\" group there was no significant post-BMT change in lung volumes and pulmonary densities. We conclude that the quantitative automatic HRCT analysis of patients with ES identified a significant reduction in pulmonary density in patients with improved pulmonary function. We speculate that, in addition to the mean volumes and densities, density percentiles may also be used as a parameter in the follow-up ofpatients with interstitial lung disease. This tool may represent a biomarker in the evaluation of interstitial lung disease treatment in patients with SSc, complementing pulmonary function tests.

Apesar de bem estabelecido em termos morfológicos, a repercussão funcional do envolvimento das pequenas vias aéreas nas pneumopatias intersticiais fibrosantes (PIF) permanece controversa. O presente estudo avaliou de maneira invasiva e não-invasiva (espirometria, volume de fechamento, variação da complacência dinâmica com a freqüência respiratória) a função das pequenas vias aéreas em portadores de PIF, comparando com grupo controle e correlacionando com índices morfométricos de biópsias. Os testes funcionais não diferenciaram portadores da doença dos controles quanto ao acomentimento das pequenas via aéreas e não se correlacionaram com os dados morfométricos / Although well known involvement of small airway in fibrosing interstitial lung disease based on morfologic issues, its functional consequences remains controversial. We present an invasive and non-invasive physiologic study for small airway function (pulmonary function tests, closing volume and frequency dependence of dynamic compliance) in patients with lung fibrosis. The physiological data were compared with normal controls and correlated with morfometric measurements from biopsies. Specific small airway function data could not show obstructive pattern when compared with normals, and did not correlate with morofmetric data

Apesar de bem estabelecido em termos morfológicos, a repercussão funcional do envolvimento das pequenas vias aéreas nas pneumopatias intersticiais fibrosantes (PIF) permanece controversa. O presente estudo avaliou de maneira invasiva e não-invasiva (espirometria, volume de fechamento, variação da complacência dinâmica com a freqüência respiratória) a função das pequenas vias aéreas em portadores de PIF, comparando com grupo controle e correlacionando com índices morfométricos de biópsias. Os testes funcionais não diferenciaram portadores da doença dos controles quanto ao acomentimento das pequenas via aéreas e não se correlacionaram com os dados morfométricos / Although well known involvement of small airway in fibrosing interstitial lung disease based on morfologic issues, its functional consequences remains controversial. We present an invasive and non-invasive physiologic study for small airway function (pulmonary function tests, closing volume and frequency dependence of dynamic compliance) in patients with lung fibrosis. The physiological data were compared with normal controls and correlated with morfometric measurements from biopsies. Specific small airway function data could not show obstructive pattern when compared with normals, and did not correlate with morofmetric data

O desenvolvimento tecnológico proporciona uma melhoria na qualidade de vida devido à facilidade, rapidez e flexibilidade no acesso à informação. Na área biomédica, a tecnologia é reconhecidamente uma importante aliada, permitindo o rápido desenvolvimento de métodos e técnicas que auxiliam o profissional na atenção à saúde. Recentes avanços na análise computadorizada de imagens médicas contribuem para o diagnóstico precoce de uma série de doenças. Nesse trabalho é apresentada uma metodologia para o desenvolvimento de um sistema computacional para caracterização de padrões em imagens pulmonares, baseado em técnicas de redes neurais artificiais. No estudo, buscou-se verificar a utilização de redes neurais auto-organizáveis como ferramenta de extração de atributos e redução de dimensionalidade de imagens radiográficas de tórax, objetivando a caracterização de lesões intersticiais de pulmão. Para a redução de dimensionalidade e extração de atributos, implementou-se um algoritmo baseado nos mapas auto-organizáveis (SOM), com algumas variações, obtendo-se uma redução dos cerca de 3 milhões de pixels que compõe uma imagem, para 240 elementos. Para a classificação dos padrões, utilizou-se uma rede Perceptron multi-camadas (MLP), validada com a metodologia leave-one-out. Com uma base contendo 79 exemplos de padrão linear, 37 exemplos de padrão nodular, 30 exemplos de padrão misto, e 72 exemplos de padrão normal, o classificador obteve a média de 89,5% de acerto, sendo 100% de classificação correta para o padrão linear, 67,5% para o padrão nodular, 63,3% para o padrão misto, e 100% para o padrão normal. Os resultados obtidos comprovam a validade da metodologia. / The technological development provides an improvement in the quality of life due to easiness, speed and flexibility in the access to the information. In the biomedical area, the technology is admitted as an important allied, allowing the fast development of methods and techniques that assist the professional in the health care. Recent advances in the computerized analysis of medical images contribute for the precocious diagnosis of a series of diseases. In this work a methodology for the development of a computational system for characterization of patterns in pulmonary images, based in techniques of artificial neural networks is presented. In the study, has searched for the verification the use of self-organizing neural networks as a feature extraction and dimensionality reduction tool of chest radiographs, willing to characterize interstitial lung disease. For the dimensionality reduction and feature extraction, an algorithm based on Self-Organizing Maps (SOM) was implemented, with some variations, getting a reduction of about 3 million pixels that it composes an image, for 240 elements. For the pattern classification, a Multilayer Perceptron (MLP) was used, validated with the leave-one-out methodology. With a database containing 79 samples of linear pattern, 37 samples of nodular pattern, 30 samples of mixed pattern, and 72 samples of normal pattern, the classifier provided an average result of 89.5% of right classification, with 100% of right classification for linear pattern, 67.5% for nodular pattern, 63.3% for mixed pattern, and 100% for normal pattern. The results prove the validity of the methodology.

Introdução: A doença intersticial pulmonar é um importante fator prognóstico na esclerose sistêmica (ES). O prognóstico das pneumonias intersticiais não específicas (NSIP) associadas às colagenoses tem sido descrito como melhor do que o da forma idiopática. Levanta-se a hipótese de que o processo de remodelamento e reparo do parênquima pulmonar nessas duas formas da doença sejam diferentes. Objetivos: Comparar os mecanismos de reparo e remodelamento entre a NSIP associada a ES e a NSIP idiopática. Observar o impacto dos mesmos nas provas de função pulmonar e na sobrevida. Métodos: Foram analisadas 40 biópsias de pacientes com o diagnóstico de NSIP (18 biópsias de NSIP associada a ES e 22 na forma idiopática). As informações clínicas e as provas de função pulmonar foram obtidas através da revisão dos prontuários. As lâminas foram revisadas por três patologistas. Foram comparadas as densidades epitelial, vascular, bem como a atividade vascular dos dois grupos utilizando o método de imuno-histoquímica. Para isso foram utilizados os anticorpos anti- citoqueratina 7 (CK-7), anti- proteína-a do surfactante (SP-A), antimarcador de célula endotelial CD-34 (CD34), e anti-molécula da adesão vascular 1 (VCAM-1). Também foi comparado o padrão de remodelamento da matriz septal e vascular, usando os métodos histoquímicos da resorcina (fibras elásticas) e picrosírius (colágeno). Uma análise estatística foi realizada comparando os resultados dos dois grupos, o impacto do remodelamento nas provas de função pulmonar e a influência na sobrevida. Resultados: A densidade das células epiteliais foi menor na NSIP-ES, do que na forma idiopática (p<0,0001). Já os pneumócitos tipo II e as células de Clara encontraram-se diminuídos no grupo idiopático (p=0,02). Uma diminuição na densidade vascular foi encontrada na NSIP-ES quando comparada à forma idiopática (p<0,0001); no entanto, a atividade vascular medida pelo VCAM-1 foi maior no grupo da NSIP-ES (p<0.0001). O conteúdo das fibras elásticas e colágeno septal, bem como o das fibras elásticas na parede vascular, estavam aumentados no grupo da ES quando comparados à forma idiopática (p=0,01; p=0,001 e p<0,0001, respectivamente). Não houve diferença estatística entre o colágeno da parede vascular, no grau de obstrução vascular ou associação entre os parâmetros de remodelamento e reparo do parênquima pulmonar na sobrevida dos dois grupos. Dentre as provas de função pulmonar, a DCO/Hb foi mais afetada no grupo da ES (59% do valor predito na ES e 97% no grupo idiopático). Foi observada uma associação direta entre a densidade vascular e a DCO/Hb (p=0,02). Após o seguimento de 36 meses, não foi observada diferença no prognóstico dos dois grupos. Conclusão: Os processos de remodelamento e reparo do parênquima pulmonar parecem ser diferentes entre os dois grupos. Apesar de o processo fibrótico ser mais intenso na NSIP-ES, isso parece não estar associado a um pior prognóstico, como tem sido descrito na forma idiopática. Como o processo de elastose e a expressão do VCAM-I são mais intensos na ES, isso sugere que o processo inflamatório tem um papel mais importante na patogênese e no processo de remodelamento e reparo da ES do que na forma idiopática. No entanto, outros estudos são necessários para validar a importância desses resultados e sua utilização para fins terapêuticos e de prognóstico / Background: The presence of Interstitial lung disease is a well recognized prognostic factor in systemic sclerosis (SSc). As the prognosis in nonspecific interstitial pneumonia (NSIP) has been described to be better in collagen vascular disorders compared to the idiopathic forms, it is conceivable that the mechanisms of repair and remodeling are different between these two forms of the disease. Objectives: To compare the mechanisms of repair and remodeling between SSc associated nonspecific pneumonia and the idiopathic form, as well as their impact on pulmonary function tests and survival rates. Methods: Biopsies from 18 patients with SSc-associated NSIP and 22 with idiopathic NSIP were analyzed. Clinical data and pulmonary function test results were obtained by retrospective chart review. All H&E slides were reviewed by three pathologists. The epithelial and vascular densities and vascular activity were compared between the two groups by immunohistochemistry with antibodies directed against cytokeratin-7, surfactant protein-a, CD34, and VCAM-1, as well as septal and vascular matrix remodeling using histochemical stains (picrosirius and resorcin). Statistical analyses were performed to compare the results of these various studies with clinical parameters (e.g. pulmonary function tests) and survival between the groups. Results: Epithelial cell density was lower in SSc-NSIP when compared with idiopathic-NSIP (p<0.0001). Type II pneumocytes and Clara cells were reduced in idiopathic NSIP (p=0.02). A decrease in microvessel density was found in SSc-NSIP compared to idiopathic-NSIP (p<0.0001). The vascular activity measured by VCAM-1 expression was higher in NSIP-SSc when compared to the idiopathic group (p<0.0001). A direct association between vascular density and DLCO/HB was found (p=0.02). Among pulmonary function tests the DLCO/HB was affected to a greater extent in the SSc group (59% of the predicted value in SSc and 97% in the idiopatic group). The content of septal collagen and elastic fibers, as well as the elastic fibers in the vascular wall, were higher in the SSc group (p=0.01, p=0.001 and p<0.0001, respectively). There were no differences in the collagen content of the vascular wall, vascular grade, or survival between the two groups. There was no difference in the survival rate between the two groups after a follow-up of 36 months. Conclusions: Alterations in the pulmonary epithelium and vasculature seem to differ in the SSc-NSIP when compared to the idiopathic form of the disease. Although the fibrotic process is more intense in the SSc group, it does not seem to affect the prognosis of these patients, contrary to what has been described in idiopatic lung fibrosis. Because the elastotic process and VCAM-1 expression are higher in the SSc group, this might suggest that inflammatory mechanisms affecting the elastic fiber system and vasculature could play a greater role in the pathogenesis and pulmonary remodeling process of SSc-NSIP than in idiopathic-NSIP. Further studies may be required to assess the significance of these findings and explore if they can provide prognostic and/or treatment information

Introdução: A doença intersticial pulmonar é um importante fator prognóstico na esclerose sistêmica (ES). O prognóstico das pneumonias intersticiais não específicas (NSIP) associadas às colagenoses tem sido descrito como melhor do que o da forma idiopática. Levanta-se a hipótese de que o processo de remodelamento e reparo do parênquima pulmonar nessas duas formas da doença sejam diferentes. Objetivos: Comparar os mecanismos de reparo e remodelamento entre a NSIP associada a ES e a NSIP idiopática. Observar o impacto dos mesmos nas provas de função pulmonar e na sobrevida. Métodos: Foram analisadas 40 biópsias de pacientes com o diagnóstico de NSIP (18 biópsias de NSIP associada a ES e 22 na forma idiopática). As informações clínicas e as provas de função pulmonar foram obtidas através da revisão dos prontuários. As lâminas foram revisadas por três patologistas. Foram comparadas as densidades epitelial, vascular, bem como a atividade vascular dos dois grupos utilizando o método de imuno-histoquímica. Para isso foram utilizados os anticorpos anti- citoqueratina 7 (CK-7), anti- proteína-a do surfactante (SP-A), antimarcador de célula endotelial CD-34 (CD34), e anti-molécula da adesão vascular 1 (VCAM-1). Também foi comparado o padrão de remodelamento da matriz septal e vascular, usando os métodos histoquímicos da resorcina (fibras elásticas) e picrosírius (colágeno). Uma análise estatística foi realizada comparando os resultados dos dois grupos, o impacto do remodelamento nas provas de função pulmonar e a influência na sobrevida. Resultados: A densidade das células epiteliais foi menor na NSIP-ES, do que na forma idiopática (p<0,0001). Já os pneumócitos tipo II e as células de Clara encontraram-se diminuídos no grupo idiopático (p=0,02). Uma diminuição na densidade vascular foi encontrada na NSIP-ES quando comparada à forma idiopática (p<0,0001); no entanto, a atividade vascular medida pelo VCAM-1 foi maior no grupo da NSIP-ES (p<0.0001). O conteúdo das fibras elásticas e colágeno septal, bem como o das fibras elásticas na parede vascular, estavam aumentados no grupo da ES quando comparados à forma idiopática (p=0,01; p=0,001 e p<0,0001, respectivamente). Não houve diferença estatística entre o colágeno da parede vascular, no grau de obstrução vascular ou associação entre os parâmetros de remodelamento e reparo do parênquima pulmonar na sobrevida dos dois grupos. Dentre as provas de função pulmonar, a DCO/Hb foi mais afetada no grupo da ES (59% do valor predito na ES e 97% no grupo idiopático). Foi observada uma associação direta entre a densidade vascular e a DCO/Hb (p=0,02). Após o seguimento de 36 meses, não foi observada diferença no prognóstico dos dois grupos. Conclusão: Os processos de remodelamento e reparo do parênquima pulmonar parecem ser diferentes entre os dois grupos. Apesar de o processo fibrótico ser mais intenso na NSIP-ES, isso parece não estar associado a um pior prognóstico, como tem sido descrito na forma idiopática. Como o processo de elastose e a expressão do VCAM-I são mais intensos na ES, isso sugere que o processo inflamatório tem um papel mais importante na patogênese e no processo de remodelamento e reparo da ES do que na forma idiopática. No entanto, outros estudos são necessários para validar a importância desses resultados e sua utilização para fins terapêuticos e de prognóstico / Background: The presence of Interstitial lung disease is a well recognized prognostic factor in systemic sclerosis (SSc). As the prognosis in nonspecific interstitial pneumonia (NSIP) has been described to be better in collagen vascular disorders compared to the idiopathic forms, it is conceivable that the mechanisms of repair and remodeling are different between these two forms of the disease. Objectives: To compare the mechanisms of repair and remodeling between SSc associated nonspecific pneumonia and the idiopathic form, as well as their impact on pulmonary function tests and survival rates. Methods: Biopsies from 18 patients with SSc-associated NSIP and 22 with idiopathic NSIP were analyzed. Clinical data and pulmonary function test results were obtained by retrospective chart review. All H&E slides were reviewed by three pathologists. The epithelial and vascular densities and vascular activity were compared between the two groups by immunohistochemistry with antibodies directed against cytokeratin-7, surfactant protein-a, CD34, and VCAM-1, as well as septal and vascular matrix remodeling using histochemical stains (picrosirius and resorcin). Statistical analyses were performed to compare the results of these various studies with clinical parameters (e.g. pulmonary function tests) and survival between the groups. Results: Epithelial cell density was lower in SSc-NSIP when compared with idiopathic-NSIP (p<0.0001). Type II pneumocytes and Clara cells were reduced in idiopathic NSIP (p=0.02). A decrease in microvessel density was found in SSc-NSIP compared to idiopathic-NSIP (p<0.0001). The vascular activity measured by VCAM-1 expression was higher in NSIP-SSc when compared to the idiopathic group (p<0.0001). A direct association between vascular density and DLCO/HB was found (p=0.02). Among pulmonary function tests the DLCO/HB was affected to a greater extent in the SSc group (59% of the predicted value in SSc and 97% in the idiopatic group). The content of septal collagen and elastic fibers, as well as the elastic fibers in the vascular wall, were higher in the SSc group (p=0.01, p=0.001 and p<0.0001, respectively). There were no differences in the collagen content of the vascular wall, vascular grade, or survival between the two groups. There was no difference in the survival rate between the two groups after a follow-up of 36 months. Conclusions: Alterations in the pulmonary epithelium and vasculature seem to differ in the SSc-NSIP when compared to the idiopathic form of the disease. Although the fibrotic process is more intense in the SSc group, it does not seem to affect the prognosis of these patients, contrary to what has been described in idiopatic lung fibrosis. Because the elastotic process and VCAM-1 expression are higher in the SSc group, this might suggest that inflammatory mechanisms affecting the elastic fiber system and vasculature could play a greater role in the pathogenesis and pulmonary remodeling process of SSc-NSIP than in idiopathic-NSIP. Further studies may be required to assess the significance of these findings and explore if they can provide prognostic and/or treatment information

In systemic sclerosis (SSc), interstitial lung disease (ILD) and engagement of the vascular system lead to increased morbidity and mortality. The aim of this thesis was to elucidate, in a consecutively included cohort of SSc (limited and diffuse) patients (n = 33), the T cell cytokine profile driving the disease in ILD and to explore the role of matrix metalloproteinase 9 (MMP-9) and its inhibitor: tissue inhibitor of metalloproteinase 1 (TIMP-1) in the extracellular matrix (ECM) degrading process leading to fibrous scarring and honey combing. Moreover, to characterize the role of nitric oxide (NO) in vascular engagement. Peripheral arterial changes cause Raynaud’s phenomenon and digital ulcers. Nitric oxide (NO) a main inducer of vasodilation is produced by endothelial nitric oxide synthase (eNOS) in response to changes in blood flow or by inflammatory cytokine inducible (i) NOS. In the vascular smooth muscle cell (VSMC) NO activates guanylate cyclase to produce cGMP, causing relaxation. We showed elevated plasma nitrate, a degradation product of NO, and increased urinary excretion of nitrate and cGMP. Plasma nitrate correlated with elevated levels of endothelial adhesion molecules: endothelial (E) selectin and vascular adhesion molecule 1, indicating that the activated endothelium is the site of NO synthesis by iNOS. Endothelial staining for E-selectin and the finding of iNOS and eNOS in SSc skin biopsies supported this notion. In SSc increased vascular stiffness may limit the NO vasodilatory effects. We found normal endothelium-dependent (i.e. flow mediated (FMD%)) and endothelium-independent (i.e. nitroglycerin-induced (NTG%)) vasodilation in the brachial artery. Radial arterial wall stiffness measured as maximum increase in pulse pressure (dP/dtmax) was increased. FMD% and especially NTG% correlated negatively and dP/dtmax positively to measures of endothelial inflammation: plasma- nitrate and adhesion molecule levels. Thus inflammatory vascular wall changes may interfere with dilation as may the presence of nitrate tolerance. We found elevated alveolar MMP-9 in both its pro- and active form in ILD. The levels correlated to decline in lung capacity, pointing at a causal relation. We suggest that neutrophils secrete MMP-9, which may degrade collagen IV, (the main constituent of basal membranes), collagen V, gelatins, proteoglycans and elastin. MMP-9 activity is partly regulated by the binding of pro- and active form to TIMP-1. Alveolar TIMP-1, which even stimulates fibroblast ECM synthesis, was increased independent of ILD. The inflammatory process in ILD is orchestrated by activated T helper (h) lymphocytes. We found a mixed Th1/Th2 reaction in SSc alveolar T cells expressing messenger for interferon gamma (Th1), IL-6 and IL-10 (both Th2). No particular cytokine mRNA profile distinguished alveolar T cells in ILD. Neutrophils invaded the bronchial epithelium, which seemed otherwise inert as levels of inflammatory cytokine sensitive transcription factors and their nuclear translocation tended to be low. The neutrophil recruitment pathway is uncertain as chemoattractants and endothelial adhesion molecules were normally expressed. In conclusion, MMP-9 probably causes degradation of lung tissue in ILD and may represent a future therapeutic target. Alveolar T cells show a mixed Th1/Th2 cytokine profile independent of ILD. Neutrophils invade the bronchial epithelium. Activated endothelium produces increased amounts of NO and adhesion molecules and the level of activation influences brachial arterial FMD% and NTG% and radial arterial compliance. Nitrate tolerance may be present.

The idiopathic inflammatory myopathies (IIMs) are a heterogeneous group of chronic muscle diseases with frequent extramuscular organ involvement that contributes to serious prognosis. The presence of autoantibodies and composition of muscle infiltrates both support autoimmune nature of the disease and pathogenic role of B lymphocytes. Besides the traditional diagnostic subgroups, autoantibody characterised phenotype subsets have been identified with presumed similar pathogenic mechanisms. The best known is the antisynthetase syndrome which is characterised by presence of myositis, antisynthetase autoantibodies (with anti-Jo-1 being the most frequent), interstitial lung disease and other extramuscular manifestations. BAFF (B cell-Activating Factor of the TNF Family) is a key factor in B cell homeostasis modulation. In high levels, it allows survival of autoreactive B cell clones and thus participates in the pathogenesis of autoimmune diseases. Its expression is induced by type I interferons (IFN-1). The aim of the PhD thesis was to explore the role of BAFF in pathogenesis of IIMs by analysis of its serum levels, the receptors for BAFF in muscle tissue, their associations to IFN-1 and expression of BAFF gene mRNA transcription variants in peripheral blood cells. Further aspect was to study a possible...

O desenvolvimento tecnológico proporciona uma melhoria na qualidade de vida devido à facilidade, rapidez e flexibilidade no acesso à informação. Na área biomédica, a tecnologia é reconhecidamente uma importante aliada, permitindo o rápido desenvolvimento de métodos e técnicas que auxiliam o profissional na atenção à saúde. Recentes avanços na análise computadorizada de imagens médicas contribuem para o diagnóstico precoce de uma série de doenças. Nesse trabalho é apresentada uma metodologia para o desenvolvimento de um sistema computacional para caracterização de padrões em imagens pulmonares, baseado em técnicas de redes neurais artificiais. No estudo, buscou-se verificar a utilização de redes neurais auto-organizáveis como ferramenta de extração de atributos e redução de dimensionalidade de imagens radiográficas de tórax, objetivando a caracterização de lesões intersticiais de pulmão. Para a redução de dimensionalidade e extração de atributos, implementou-se um algoritmo baseado nos mapas auto-organizáveis (SOM), com algumas variações, obtendo-se uma redução dos cerca de 3 milhões de pixels que compõe uma imagem, para 240 elementos. Para a classificação dos padrões, utilizou-se uma rede Perceptron multi-camadas (MLP), validada com a metodologia leave-one-out. Com uma base contendo 79 exemplos de padrão linear, 37 exemplos de padrão nodular, 30 exemplos de padrão misto, e 72 exemplos de padrão normal, o classificador obteve a média de 89,5% de acerto, sendo 100% de classificação correta para o padrão linear, 67,5% para o padrão nodular, 63,3% para o padrão misto, e 100% para o padrão normal. Os resultados obtidos comprovam a validade da metodologia. / The technological development provides an improvement in the quality of life due to easiness, speed and flexibility in the access to the information. In the biomedical area, the technology is admitted as an important allied, allowing the fast development of methods and techniques that assist the professional in the health care. Recent advances in the computerized analysis of medical images contribute for the precocious diagnosis of a series of diseases. In this work a methodology for the development of a computational system for characterization of patterns in pulmonary images, based in techniques of artificial neural networks is presented. In the study, has searched for the verification the use of self-organizing neural networks as a feature extraction and dimensionality reduction tool of chest radiographs, willing to characterize interstitial lung disease. For the dimensionality reduction and feature extraction, an algorithm based on Self-Organizing Maps (SOM) was implemented, with some variations, getting a reduction of about 3 million pixels that it composes an image, for 240 elements. For the pattern classification, a Multilayer Perceptron (MLP) was used, validated with the leave-one-out methodology. With a database containing 79 samples of linear pattern, 37 samples of nodular pattern, 30 samples of mixed pattern, and 72 samples of normal pattern, the classifier provided an average result of 89.5% of right classification, with 100% of right classification for linear pattern, 67.5% for nodular pattern, 63.3% for mixed pattern, and 100% for normal pattern. The results prove the validity of the methodology.