EGFR TKIs are standard therapy for advanced NSCLC. In order to define their role in early disease, we implemented a phase II trial of neoadjuvant gefitinib in clinical stage I NSCLC. Tumour shrinkage was seen in 43% of patients, with 11% achieving RECIST partial response (PR). Analysis of molecular markers showed EGFR TKD mutations in 17% of cases, being the only associated with PR. For the first time we defined the histopathological response of NSCLC to these agents, characterized by reduction in tumour cellularity and proliferative index as well as presence of non-mucinous BAC histology. Clinical PR tumours also presented large areas of stromal fibrosis with presence of focal residual tumour. In a characterization of intracellular signalling response, EGFR dephosphorylation in the residues Y1068 and Y1173 was not concordant and only the former was significantly reduced. pAkt Ser473/Akt and Thr308/Akt ratios were significantly reduced but observed among both, clinical responders and resistant patients. Interestingly, reduction in pEGFR Y1068 was significantly associated with increase in tumour cellularity (p=0.047), Ki-67 index (p=0.018) and tumour growth (p=0.019) with a residual perinuclear localization been detected, suggesting a novel mechanism of resistance involving receptor internalization. Finally, we determined that the EGFR protein remains stable up to one hour of post resection ischemia but two to three tumour samples are necessary for an adequate tumour representation. Furthermore, EGFR cytoplasmic compartment presented the best association with clinical response in our cohort. Taking all together, we were able to generate the first clinical trial exploring the use of an EGFR TKI in early NSCLC, characterizing for the first time the histopathological and signalling responses to these agents with an evidence of a potential novel mechanism of resistance. Finally, we observed that multiple samples collection for an adequate tumour representation, and assessment of the cytoplasmic compartment, are warrant.

EGFR TKIs are standard therapy for advanced NSCLC. In order to define their role in early disease, we implemented a phase II trial of neoadjuvant gefitinib in clinical stage I NSCLC. Tumour shrinkage was seen in 43% of patients, with 11% achieving RECIST partial response (PR). Analysis of molecular markers showed EGFR TKD mutations in 17% of cases, being the only associated with PR. For the first time we defined the histopathological response of NSCLC to these agents, characterized by reduction in tumour cellularity and proliferative index as well as presence of non-mucinous BAC histology. Clinical PR tumours also presented large areas of stromal fibrosis with presence of focal residual tumour. In a characterization of intracellular signalling response, EGFR dephosphorylation in the residues Y1068 and Y1173 was not concordant and only the former was significantly reduced. pAkt Ser473/Akt and Thr308/Akt ratios were significantly reduced but observed among both, clinical responders and resistant patients. Interestingly, reduction in pEGFR Y1068 was significantly associated with increase in tumour cellularity (p=0.047), Ki-67 index (p=0.018) and tumour growth (p=0.019) with a residual perinuclear localization been detected, suggesting a novel mechanism of resistance involving receptor internalization. Finally, we determined that the EGFR protein remains stable up to one hour of post resection ischemia but two to three tumour samples are necessary for an adequate tumour representation. Furthermore, EGFR cytoplasmic compartment presented the best association with clinical response in our cohort. Taking all together, we were able to generate the first clinical trial exploring the use of an EGFR TKI in early NSCLC, characterizing for the first time the histopathological and signalling responses to these agents with an evidence of a potential novel mechanism of resistance. Finally, we observed that multiple samples collection for an adequate tumour representation, and assessment of the cytoplasmic compartment, are warrant.

This dissertation focuses on developing imaging informatics algorithms for clinical decision support systems (CDSSs) based on histopathological whole-slide images (WSIs). Currently, histopathological analysis is a common clinical procedure for diagnosing cancer presence, type, and progression. While diagnosing patients using biopsy slides, pathologists manually assess nuclear morphology. However, making decisions manually from a slide with millions of nuclei can be time-consuming and subjective. Researchers have proposed CDSSs that help in decision making but they have limited reproducibility. The development of robust CDSSs for WSIs faces several informatics challenges: (1) Lack of robust segmentation methods for histopathological images, (2) Semantic gap between quantitative information and pathologist’s knowledge, (3) Lack of batch-invariant imaging informatics methods, (4) Lack of knowledge models for capturing informative patterns in large WSIs, and (5) Lack of guidelines for optimizing and validating diagnostic models. I conducted advanced imaging informatics research to overcome these challenges and developed novel methods to extract information from WSIs, to model knowledge embedded in large histopathological datasets, such as The Cancer Genome Atlas (TCGA), and to assist decision making with biological and clinical validation. I validated my methods for two applications: (1) diagnosis of histopathology-based endpoints such as subtype and grade and (2) prediction of clinical endpoints such as metastasis, stage, lymphnode spread, and survival. The statistically emergent feature subsets in the diagnostic models for histopathology-based endpoints were concordant with pathologists’ knowledge.

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2013-04-19T16:30:30Z No. of bitstreams: 1 Marina Loyola Dantas Aspectos comparativos....pdf: 35265598 bytes, checksum: c8a29ec5c8fd370f04c04a980fb43507 (MD5) / Made available in DSpace on 2013-04-19T16:30:30Z (GMT). No. of bitstreams: 1 Marina Loyola Dantas Aspectos comparativos....pdf: 35265598 bytes, checksum: c8a29ec5c8fd370f04c04a980fb43507 (MD5) Previous issue date: 2012 / Universidade Federal da Bahia. Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz / A forma clínica mais frequente das leishmanioses é a leishmaniose cutânea, que acomete somente a pele e constitui um importante problema de saúde no Brasil. A leishmaniose cutânea caracteriza-se por lesão cutânea ulcerada única: leishmaniose cutânea localizada, que pode regredir espontaneamente ou se disseminar com múltiplas úlceras e pápulas e que aparecem em diferentes locais. A presença de disseminação caracteriza a leishmaniose cutânea disseminada. Investigar, no tecido, células que compõem o infiltrado inflamatório em lesões de pele na leishmaniose e caracterizar a resposta imune e sua correlação com a extensão total da inflamação in situ pode contribuir para aprofundar o entendimento da leishmaniose cutânea. Neste estudo, através da imunomarcação e quantificação de células por imunoistoquímica e HE, e análise da extensão da inflamação, foi comparado a histopatologia e presença de células inflamatórias CD4+, CD8+, CD68+, CD20+, plasmócitos e neutrófilos, e células granzima B+ em biópsias de pacientes com leishmaniose cutânea tardia (úlcera tardia e úlcera recente) e leishmaniose disseminada (úlcera e pápula). A análise dos padrões histomorfológicos mostrou semelhança entre os quatro grupos de biópsias analisados. Avaliando o número e tipo de células presentes, o predomínio foi de macrófagos e linfócitos. As úlceras da leishmaniose cutânea clássica e disseminada apresentaram média maior de inflamação, maior frequência de linfócitos T CD4+, T CD8+, macrófagos, linfócitos B CD20+ e plasmócitos que úlceras recentes e pápulas. Estas, por sua vez, ao contrário das úlceras tardias de ambas formas clínicas, tiveram correlação positiva entre o aumento do infiltrado inflamatório e T CD4+ e T CD8+, e não correlação com granzima B e neutrófilos. Os plasmócitos se mostraram elementos quase constantes no infiltrado das lesões em todos os grupos, e sua frequência foi maior que de linfócitos B. Seguindo o mesmo padrão descrito nos linfócitos B, os plasmócitos não apresentam correlação com o influxo de infiltrado inflamatório entre os grupos. A frequência de macrófagos é vista nos dois estágios avaliados da doença e nas duas formas clínicas de forma semelhante, porém com uma tendência para maior presença em lesões de LD. A análise de neutrófilos revelou semelhança da frequência dessas células em todos os tipos de lesões em ambas formas clínicas, com as pápulas tendendo para uma menor quantidade. Portanto, o desenvolvimento das lesões ocorrem com o influxo de células inflamatórias, como linfócitos T CD4+ e T CD8+ e a resposta imune celular é mais intensa em lesões crônicas da leishmaniose cutânea localizada e disseminada do que em lesões localizadas recentes e pápulas da leishmaniose disseminada. Diferenças in situ na resposta inflamatória destas duas formas clínicas e quatro espectros de lesão da leishmaniose humana podem elucidar o papel de células no local da lesão e contribuir para o entendimento da patogênese da leishmaniose. / Cutaneous leishmaniasis is the most frequent clinical form of leishmaniasis, which affects only the skin and is an important health problem in Brazil. Cutaneous leishmaniasis is characterized by single ulcerated skin lesion: localized cutaneous leishmaniasis, which may regress spontaneously or spread with multiple ulcers and papules that appear in different parts of the body. The presence of dissemination features disseminated leishmaniasis. Investigate tissue cells from inflammatory infiltrate in skin lesions in leishmaniasis and characterize the immune response and its correlation with the total extent of inflammation in situ may contribute to deepen the understanding of cutaneous leishmaniasis. In this study, immunostaining and cells quantification by immunohistochemistry and HE and analysis of inflammation extention was compared with histopathology and CD4+, CD8+, CD68+, CD20+, plasma cells, neutrophils and granzyme B+ cells in biopsies of patients with localized cutaneous leishmaniasis (late ulcer and recent ulcer) and disseminated leishmaniasis (ulcers and papules). The histopathological patterns analysis was similar among the four biopsies groups analyzed. Macrophages and lymphocytes were the predominant cells. The ulcers of localized cutaneous leishmaniasis and disseminated leishmaniasis presented higher mean inflammation, increased frequency of CD4+ and CD8+ T cells, macrophages, B lymphocytes CD20+ and plasma cells than recent ulcers and papules. These, in turn, unlike late ulcers of both clinical forms, had positive correlation between the increase in inflammatory infiltrate and CD4+ and CD8+ T cells, differing in Granzyme B and neutrophils. Plasma cells were almost constant in lesion infiltrate in all groups and was higher than the frequency of B lymphocytes. Following the same pattern described in B lymphocytes, plasma cells did not show an association with the influx of inflammatory infiltrate between groups. The frequency of macrophages is seen in both stages of the disease and in the two clinical forms similarly, but with a tendency to be increased in disseminated lesihmaniasis lesions. The analysis revealed similarity of neutrophils frequency in all types of lesions, with papules tending to a lesser extent. Therefore, the development of lesions occur with the influx of inflammatory cells such as CD4+ and CD8+ T cells and cellular immune response is more intense in chronic lesions of localized cutaneous leishmaniasis and disseminated leishmaniasis than recent localized lesions and papules from disseminated leishmaniasis. Differences of inflammatory response in situ in these two clinical forms and four spectra of human leishmaniasis lesions may elucidate the role of cells at the lesion site and contribute to the understanding of leishmaniasis pathogenesis.

Submitted by Edineia Teixeira (edineia.teixeira@unioeste.br) on 2018-03-02T18:14:01Z No. of bitstreams: 2 Mayara_Neves 2017.pdf: 1691652 bytes, checksum: b3023a3c776f7cbfd5a2cdf3d7e74764 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-03-02T18:14:01Z (GMT). No. of bitstreams: 2 Mayara_Neves 2017.pdf: 1691652 bytes, checksum: b3023a3c776f7cbfd5a2cdf3d7e74764 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-10-03 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Aquatic environments are much more dependent on their watersheds, especially for the allochthonous input of energy, as well as subject to contamination by various stressors. In this context, this study aimed to evaluate histopathological biomarkers of liver and gills of catfish endemic, in order to test the hypothesis that in environments under intense land use by agricultural activities occur histopathological alterations more severe. Samples were collected by electrofishing technique in seven streams in the Lower Iguaçu basin quarterly from August 2015 to February 2016. Gills and livers were processed according to routine histological and examined by light microscopy. The histopathological alterations observed in fish from the streams with higher percentage of natural vegetation cover were considered modest and indicated normal functioning of the organ (edema, hyperplasia, leukocyte infiltration). In streams with higher agricultural influence, were registered moderate damage to severe (aneurysm, vacuolization and cytoplasmic degeneration, pyknotic nucleus). The abundance of chloride cells was significantly increased in the gills of A. mullerae collected in rural streams. In addition, in most streams, mucous cells were more abundant in the rainy period. Significant differences were observed in histopathological index (HI) of gill and liver where severe histopathological alterations occurred in fish whose streams exhibit greater influence agricultural. Alterations were more severe in the liver than in gills, indeed related to its key role in detoxification of xenobiotics. We conclude that the increased agricultural use with reduction of riparian forest cause harmful effects in fish. Thus, our work provides important contributions to the conservation and management of natural resources, since it is a pioneer in demonstrating the effect of gradients of agricultural influence in field conditions on biomarkers of an endemic species / Os ambientes aquáticos são ecossistemas dependentes dos vários usos e ocupação da bacia, sendo inclusive, sujeitos a contaminação por vários poluentes. Nesse contexto, o presente estudo teve como objetivo avaliar biomarcadores histopatológicos de brânquias e fígado de um cascudo, Ancistrus mullerae, a fim de testar a hipótese de que em ambientes sob intensa utilização do entorno por atividades agrícolas, ocorram histopatologias mais severas. As amostragens foram realizadas por meio da técnica de pesca elétrica, em sete riachos, na bacia do baixo Iguaçu, em agosto/2015 e fevereiro/2016. Brânquias e fígados foram processados de acordo com a rotina histológica e analisados por meio de microscopia de luz. As alterações histopatológicas observadas nos peixes dos riachos com maior porcentagem de cobertura vegetal nativa foram consideradas moderadas e indicaram o funcionamento normal do órgão (edema, hiperplasia, infiltração leucocitária). Em riachos com maior influência agrícola, foram registrados danos moderados a graves (aneurisma, vacuolização e degeneração citoplasmática, núcleo picnótico). A abundância de células de cloreto aumentou significativamente nas brânquias de A. mullerae coletados em riachos rurais. Além disso, na maioria dos riachos, as células de muco foram mais abundantes no período chuvoso. Observaram-se diferenças significativas no índice histopatológico (IH) de brânquia e fígado, onde ocorreram alterações histopatológicas graves em peixes cujos riachos apresentaram maior influência agrícola. As alterações foram mais graves no fígado do que nas brânquias, fato relacionado com seu papel fundamental na desintoxicação dos xenobióticos. Concluímos que o maior uso e ocupação do solo por atividades agrícolas causam efeitos nocivos nos peixes. Assim, o nosso trabalho fornece importantes contribuições para a conservação e manejo dos recursos naturais, pois é pioneiro em demonstrar o efeito de gradientes de influência agrícola em condições de campo em biomarcadores de espécies endêmicas.

Breast cancer is the most common type of cancer in the world, and it is the second deadliest cancer for females. In the fight against breast cancer, early detection plays a large role in saving people’s lives. In this work, an image classifier is designed to diagnose breast tumors as benign or malignant. The classifier is designed with a neural network and trained on the BreakHis dataset. After creating the initial design, a variety of methods are used to try to improve the performance of the classifier. These methods include preprocessing, increasing the number of training epochs, changing network architecture, and data augmentation. Preprocessing includes changing image resolution and trying grayscale images rather than RGB. The tested network architectures include VGG16, ResNet50, and a custom structure. The final algorithm creates 50 classifier models and keeps the best one. Classifier designs are primarily judged on the classification accuracies of their best model and their median model. Designs are also judged on how consistently they produce their highest performing models. The final classifier design has a median accuracy of 93.62% and best accuracy of 96.35%. Of the 50 models generated, 46 of them performed with over 85% accuracy. The final classifier design is compared to the works of two groups of researchers who created similar classifiers for the same dataset. This will show that the classifier performs at the same level or better than the classifiers designed by other researchers. The classifier achieves similar performance to the classifier made by the first group of researchers and performs better than the classifier from the second. Finally, the learned lessons and future steps are discussed.

No / Nowadays, there is no argument that deep learning algorithms provide impressive results in many applications of medical image analysis. However, data scarcity problem and its consequences are challenges in implementation of deep learning for the digital histopathology domain. Deep transfer learning is one of the possible solutions for these challenges. The method of off-the-shelf features extraction from pre-trained convolutional neural networks (CNNs) is one of the common deep transfer learning approaches. The architecture of deep CNNs has a significant role in the choice of the optimal learning transferable features to adopt for classifying the cancerous histopathological image. In this study, we have investigated three pre-trained CNNs on ImageNet dataset; ResNet-50, DenseNet-201 and ShuffleNet models for classifying the Breast Cancer Histopathology (BACH) Challenge 2018 dataset. The extracted deep features from these three models were utilised to train two machine learning classifiers; namely, the K-Nearest Neighbour (KNN) and Support Vector Machine (SVM) to classify the breast cancer grades. Four grades of breast cancer were presented in the BACH challenge dataset; these grades namely normal tissue, benign tumour, in-situ carcinoma and invasive carcinoma. The performance of the target classifiers was evaluated. Our experimental results showed that the extracted off-the-shelf features from DenseNet-201 model provide the best predictive accuracy using both SVM and KNN classifiers. They yielded the image-wise classification accuracy of 93.75% and 88.75% for SVM and KNN classifiers, respectively. These results indicate the high robustness of our proposed framework.

No description available.

No / Clinical morphological analysis of histopathological specimens is a successful manner for diagnosing benign and malignant diseases. Analysis of glandular architecture is a major challenge for colon histopathologists as a result of the difficulty of identifying morphological structures in glandular malignant tumours due to the distortion of glands boundaries, furthermore the variation in the appearance of staining specimens. For reliable analysis of colon specimens, several deep learning methods have exhibited encouraging performance in the glands automatic segmentation despite the challenges. In the histopathology field, the vast number of annotation images for training the deep learning algorithms is the major challenge. In this work, we propose a trainable Convolutional Neural Network (CNN) from end to end for detecting the glands automatically. More specifically, the Modified Res-U-Net is employed for segmenting the colorectal glands in Haematoxylin and Eosin (H&E) stained images for challenging Gland Segmentation (GlaS) dataset. The proposed Res-U-Net outperformed the prior methods that utilise U-Net architecture on the images of the GlaS dataset.

Introduction: Les études populationnelles sur le cancer nécessitent un recensement de référence fiable et exhaustif, en théorie possible à partir d'un recueil histologique. Méthode: Depuis 2005, toutes les structures d'anatomopathologie des Alpes-Maritimes adressent les codes ADICAP des tumeurs malignes et invasives et identifiants patients. L'exhaustivité pour les cancers du sein et colorectaux des 50-75 ans a été évalué par méthode de capture recapture en modélisation log-linéaire et en Bayesien à partir des cas communs ou non dépistés et vus en Réunion de Concertation Pluridisciplinaire. RésultatUn programme d'assurance qualité a permis de s'assurer de la fiabilité des données recueillies.L'estimation de l'exhaustivité était de plus de 90 % pour les cancers du sein et colorectaux des 50-75 ans. Les taux observés sur le département des Alpes-Maritimes, comparés aux taux estimés en France, se sont révélés cohérents.Enfin, la base a été utilisée pour déterminer l'existant les lésions prénéoplasiques du col de l'utérus avant la vaccination anti-HPV. ConclusionCe travail conclut à l'intérêt d'un recueil histologique des cas de cancers incidents. / Introduction Cancer population studies require reliable and complete baseline data, which should theoretically be available by collecting histopathology records.Method Since 2005, all histopathology laboratories from Alpes-Maritimes address ADICAP codes for invasive cancer and patient identifiers. The completeness of such a collection was evaluated using capture-recapture analysis based on three data sources concerning breast and colorectal cancers with the number of cases which were common or not between sources recording screened, diagnosed and treated cancers in the French Alpes Maritimes districtResult Data quality for the ADICAP code database may be considered satisfactoryThe estimated completeness of cancer records collected from histopathology laboratories was higher than 90%.Rates observed in the Alpes-Maritimes, compared with estimated rates in France have proven consistent. Rates of CIN for the entire female population of the Alpes-Maritimes in 2006 has been established.Conclusion A verified and validated histopathology data collection may be useful for cancer population studies.