Recent studies suggest that factor (F) XII plays a key role in thrombus stabilization and growth but is dispensable for hemostasis. We have previously shown that histidine-rich glycoprotein (HRG), a protein present in platelets and plasma, binds FXIIa and inhibits FXII autoactivation and FXIIa-mediated activation of FXI, thereby downregulating thrombosis. HRG binds various ligands, including FXIIa, fibrin(ogen), nucleic acids and polyphosphate (polyP). Studies have shown that polyP, released from activated platelets, and artificial surfaces like catheters, can promote FXII activation. This suggests that HRG can downregulate the activation of the contact system. This thesis aims to determine the potential mechanisms by which HRG modulates platelet function and thrombosis induced by polyP or catheters. We show that HRG binds polyP with high affinity and inhibits the procoagulant, prothrombotic and cardiotoxic effects of polyP via at least two mechanisms. First, HRG binds polyP and neutralizes its procoagulant activities and cytotoxic effects. Second, HRG binds FXIIa and attenuates its capacity to promote autoactivation and activate FXI. Also, we identify that HRG serves as a molecular brake for the contact system by attenuating the procoagulant activity of FXIIa regardless of whether FXII activation is triggered systemically with polyP or occurs locally on the surface of catheters. Our studies have identified HRG as a novel ligand for platelet receptor GPIbα on resting platelets, and upon activation, it competes with fibrinogen for binding to GPIIb/IIIa integrin, thereby inhibiting platelet aggregation. These findings suggest that HRG may modulate coagulation as well as platelet function. Therefore, supplementation with HRG or HRG analogs may serve as a potential therapeutic option to attenuate polyP or catheter-induced thrombosis without perturbing hemostasis. / Dissertation / Doctor of Philosophy (PhD)

Yes / Introduction: We examined the relationship between Apolipoprotein E (APOE) genotype and n-3 highly unsaturated fatty acid (HUFA) levels in participants of the seAFOod trial, who were undergoing colonoscopy surveillance after removal of colorectal polyps. Methods: Baseline and on-treatment (eicosapentaenoic acid [EPA] 2 g daily or placebo for 6 months) levels of n-3 HUFAs, and plasma 18-hydroxyeicosapentaenoic acid (HEPE), were analysed according to APOE genotype (based on polymorphisms rs429358 and rs7412) in 584 participants. Results: Before treatment, APOE2/2 individuals had lower levels, and APOE4/4 participants had higher levels, of n-3 HUFAs, including EPA, than APOE3/3 counterparts (P < 0.01 for the APOE2/2 versus APOE4/4 comparison). After EPA supplementation, n-3 HUFA levels were not significantly different when stratified by APOE genotype, although APOE4 carriers displayed lower plasma 18-HEPE levels than individuals without an APOE4 allele (P = 0.002). Conclusions: APOE genotype is associated with differential n-3 HUFA and 18-HEPE levels in individuals with multiple colorectal polyps. / This project (NIHR128210) was funded by the Efficacy and Mechanism Evaluation (EME) Programme, an MRC and NIHR partnership. The views expressed in this publication are those of the authors and not necessarily those of the MRC, NIHR or the Department of Health and Social Care. MAH is a NIHR Senior Investigator. MAH is supported by Cancer Research UK grant C23434/A24939.

Yes / Background: The omega-3 polyunsaturated fatty acid eicosapentaenoic acid (EPA) and aspirin both have proof of concept for colorectal cancer chemoprevention, aligned with an excellent safety profile. Therefore, we aimed to test the efficacy of EPA and aspirin, alone and in combination and compared with a placebo, in individuals with sporadic colorectal neoplasia detected at colonoscopy. Methods: In a multicentre, randomised, double-blind, placebo-controlled, 2 × 2 factorial trial, patients aged 55–73 years who were identified during colonoscopy as being at high risk in the English Bowel Cancer Screening Programme (BCSP; ≥3 adenomas if at least one was ≥10 mm in diameter or ≥5 adenomas if these were <10 mm in diameter) were recruited from 53 BCSP endoscopy units in England, UK. Patients were randomly allocated (1:1:1:1) using a secure web-based server to receive 2 g EPA-free fatty acid (FFA) per day (either as the FFA or triglyceride), 300 mg aspirin per day, both treatments in combination, or placebo for 12 months using random permuted blocks of randomly varying size, and stratified by BCSP site. Research staff and participants were masked to group assignment. The primary endpoint was the adenoma detection rate (ADR; the proportion of participants with any adenoma) at 1 year surveillance colonoscopy analysed in all participants with observable follow-up data using a so-called at-the-margins approach, adjusted for BCSP site and repeat endoscopy at baseline. The safety population included all participants who received at least one dose of study drug. The trial is registered with the International Standard Randomised Controlled Trials Number registry, number ISRCTN05926847. Findings: Between Nov 11, 2011, and June 10, 2016, 709 participants were randomly assigned to four treatment groups (176 to placebo, 179 to EPA, 177 to aspirin, and 177 to EPA plus aspirin). Adenoma outcome data were available for 163 (93%) patients in the placebo group, 153 (85%) in the EPA group, 163 (92%) in the aspirin group, and 161 (91%) in the EPA plus aspirin group. The ADR was 61% (100 of 163) in the placebo group, 63% (97 of 153) in the EPA group, 61% (100 of 163) in the aspirin group, and 61% (98 of 161) in the EPA plus aspirin group, with no evidence of any effect for EPA (risk ratio [RR] 0·98, 95% CI 0·87 to 1·12; risk difference –0·9%, –8·8 to 6·9; p=0·81) or aspirin (RR 0·99 (0·87 to 1·12; risk difference –0·6%, –8·5 to 7·2; p=0·88). EPA and aspirin were well tolerated (78 [44%] of 176 had ≥1 adverse event in the placebo group compared with 82 [46%] in the EPA group, 68 [39%] in the aspirin group, and 76 [45%] in the EPA plus aspirin group), although the number of gastrointestinal adverse events was increased in the EPA alone group at 146 events (compared with 85 in the placebo group, 86 in the aspirin group, and 68 in the aspirin plus placebo group). Six upper-gastrointestinal bleeding events were reported across the treatment groups (two in the EPA group, three in the aspirin group, and one in the placebo group). Interpretation Neither EPA nor aspirin treatment were associated with a reduction in the proportion of patients with at least one colorectal adenoma. Further research is needed regarding the effect on colorectal adenoma number according to adenoma type and location. Optimal use of EPA and aspirin might need a precision medicine approach to adenoma recurrence. / Efficacy and Mechanism Evaluation Programme, a UK Medical Research Council and National Institute for Health Research partnership. / Research Development Fund Publication Prize Award winner, November 2018.

Les protéines de type prion, contenant des Séquences en acides aminés de Faible Complexité (SFC), ont tendance à s’agréger et à former des compartiments non-membranaires dans la cellule. Ces derniers ont des propriétés physiques communes à celles des liquides, telles que la capacité de mouiller les surfaces, de s’écouler et de fusionner avec d’autres corps liquides. Dans cette étude, nous avons démontré que la protéine Hrp1 forme, in vitro, des gouttes de différentes tailles via une transition de phase liquide à liquide, et ce, uniquement lorsqu’elle est exposée à un milieu chargé négativement. Exclusivement dans ce même milieu, nous avons aussi observé que le domaine SFC de Hrp1 s’assemble et forme une matière de type gel. Sur la base de ces observations, nous avons émis l’hypothèse que la tendance des systèmes moléculaires à former des compartiments liquides in vivo peut être influencée par la présence, dans le cytosol, de polyélectrolytes chargés négativement tels que l'ADN, l'ARN et les polyphosphates (PolyP). En utilisant la levure comme modèle cellulaire et des techniques de microscopie à fluorescence, nous nous sommes focalisés sur l’étude du rôle des PolyP dans l'assemblage des P-bodies. Les P-bodies ont été choisis comme système moléculaire de référence in vivo, étant des corps qui, après une transition de phase, se trouvent dans le cytosol sous forme de gouttes. Nous avons démontré que la déplétion du phosphate et la délétion du gène vtc4, responsable de la synthèse des PolyP dans la levure, n’ont pas d’influence dans la formation des P-bodies. Nous avons aussi remarqué que les PolyP et la protéine Edc3, une des composantes principales des P-bodies, ne sont pas co-localisés dans la cellule. Cette étude préliminaire nous suggère un manque de corrélation entre la formation des P-bodies et la présence de PolyP dans la cellule. Cependant, pour confirmer nos observations, des expériences complémentaires doivent être envisagées, en considérant d’autres composantes des P-bodies, tel que Lsm4, ou en analysant, in vivo, les effets des PolyP sur d’autres systèmes moléculaires de nature liquide. / Prion-like proteins containing Low Complexity Sequences (LCSs) have the propensity to aggregate and form membrane-less compartments in the cell. These proteins form droplets that have liquid features such as wetting, dripping and fusion. In this study, we demonstrated that the prion domain-containing protein Hrp1 forms droplets of different sizes in the presence of negatively charged polymers via liquid-liquid phase separation, whereas under the same conditions, the prion-like domain PolyQ/N of Hrp1 forms a gel-like material. Based on these findings, we hypothesize that droplets in vivo could be modulated by negatively charged polyelectrolytes found in the cell such as DNA, RNA and polyphosphate (PolyP). My goal was to examine the role of the polyanionic nature of PolyP on the assembly of P-bodies using Saccharomyces cerevisiae as a cellular model and fluorescence microscopy. We chose to study processing (P)- bodies, based on previous findings that these cellular subcompartments are formed by liquid-liquid phase separation of component proteins in the cytoplasm. We found that depleting phosphate from the media and deleting vtc4 gene, which is responsible for PolyP synthesis, did not have any effect on P-body formation. In addition, we demonstrated that PolyP and the protein Edc3, a core component of P-bodies, do not colocalize. Our data suggest that PolyP does not affect P-body formation. However, further and complementary studies have to be performed to confirm that PolyP have no effects on other membrane-less organelles.

No description available.

Segundo o Instituto Nacional do Câncer (INCA), o câncer de colorretal é o terceiro tipo de câncer mais comum entre os homens e o segundo entre as mulheres. Atualmente a avaliação visual feita por um patologista é o principal método utilizado para o diagnóstico de doenças a partir de imagens microscópicas obtidas por meio de amostras em exames convencionais de biópsia. A utilização de técnicas de processamento computacional de imagens possibilita a identificação de elementos e a extração de características, o que contribui com o estudo da organização estrutural dos tecidos e de suas variações patológicas, levando a um aumento da precisão no processo de tomada de decisão. Os conceitos e técnicas envolvendo redes complexas são recursos valiosos para o desenvolvimento de métodos de análise estrutural de componentes em imagens médicas. Dentro dessa perspectiva, o objetivo geral deste trabalho foi o desenvolvimento de um método capaz de realizar o processamento e a análise de imagens obtidas em exames de biópsias de tecidos de pólipo de cólon para classificar o grau de atipia da amostra, que pode variar em: sem atipia, baixo grau, alto grau e câncer. Foram utilizadas técnicas de processamento, incluindo um conjunto de operadores morfológicos, para realizar a segmentação e a identificação de estruturas glandulares. A seguir, procedeu-se à análise estrutural baseada na identificação das glândulas, usando técnicas de redes complexas. As redes foram criadas transformado os núcleos das células que compõem as glândulas em vértices, realizando a ligação dos mesmos com 1 até 20 arestas e a extração de medidas de rede para a criação de um vetor de características. A fim de avaliar comparativamente o método proposto, foram utilizados extratores clássicos de características de imagens, a saber, Descritores de Haralick, Momentos de Hu, Transformada de Hough, e SampEn2D. Após a avaliação do método proposto em diferentes cenários de análise, o valor de acurácia geral obtida pelo mesmo foi de 82.0%, superando os métodos clássicos. Conclui-se que o método proposto para classificação de imagens histológicas de pólipos utilizando análise estrutural baseada em redes complexas mostra-se promissor no sentido de aumentar a acurácia do diagnóstico de câncer colorretal / According to the National Cancer Institute (INCA), colorectal cancer is the third most common cancer among men and the second most common cancer among women. Currently the main method used for the diagnosis of diseases from microscopic images obtained through samples in conventional biopsy tests are the visual evaluation made by a pathologist. The use of computational image processing techniques allows the identification of elements and the extraction of characteristics, which contributes to the study of the structural organization of tissues and their pathological variations, leading to an increase of precision in the decision making process. Concepts and techniques involving complex networks are valuable resources for the development of structural analysis methods of components in medical images. In this perspective, the general objective of this work was the development of a method capable of performing the image processing and analysis obtained in biopsies of colon polyp tissue to classify the degree of atypia of the sample, which may vary in: without atypia, low grade, high grade and cancer. Processing techniques including a set of morphological operators, were used to perform the segmentation and identification of glandular structures. Next, structural analysis was performed based on glands identification, using complex network techniques.The networks were created transforming the core of the cells that make up the glands in vertices, making the connection of the same with 1 to 20 edges and the extraction of network measurements to create a vector of characteristics. In order to comparatively evaluate the proposed method, classical image characteristic extractors were used, namely, Haralicks Descriptors, Hus Moments, Hough Transform, and SampEn2D. After the evaluation of the proposed method in different analysis scenarios, the overall accuracy value obtained by it was 82.0%, surpassing the classical methods. It is concluded that the proposed method for the classification of histological images of polyps using structural analysis based on complex networks is promising in order to increase the accuracy of the diagnosis of colorectal cancer

Introdução: Embora a fisiopatogenia da rinossinusite crônica (RSC) ainda não esteja totalmente elucidada, em virtude da sua heterogeneidade e multifatorialidade, existe um crescente corpo de evidências apontando que as bactérias exerçam um papel significativo na gênese ou perpetuação da inflamação crônica. Uma das possíveis formas de atuação são os biofilmes bacterianos, comumente encontrados em pacientes com RSC e que estão relacionados com má evolução clínica. Ainda, existem evidências de que algumas espécies bacterianas, especialmente o Staphylococcus aureus (S. aureus), são capazes de invadir as células epiteliais e permanecerem viáveis em seu interior. Por fim, tem se demonstrado que pacientes RSC com pólipo nasal (RSCcPN) revelam alta associação com a presença de superantígenos estafilocócicos na mucosa respiratória, responsáveis pela estimulação acentuada de respostas inflamatórias locais. Apesar de essas diferentes formas bacterianas estarem bem descritas na RSC, não se sabe ainda com clareza como elas estão associadas nesses indivíduos. Objetivos: Avaliar a associação entre a presença de biofilmes, bactérias intracelulares e superantígenos estafilocócicos em pacientes com RSC (com e sem pólipo nasal), comparados com o grupo controle. Casuística e Métodos: Avaliou-se a prevalência de biofilmes bacterianos, bactérias intracelulares e presença de superantígenos bacterianos em indivíduos com RSCcPN, sem pólipo nasal (RSCsPN) e controles, analisando a associação de distribuição de prevalência desses diferentes grupos (teste exato de Fisher, nível de significância quando p<0,05). Os biofilmes foram definidos por características morfológicas à microscopia eletrônica de varredura (MEV), as bactérias intracelulares foram analisadas por microscopia eletrônica de transmissão (MET) e hibridização fluorescente in situ (FISH) para S. aureus, e superantígenos de S. aureus A-E foram quantificados pela técnica de ELISA (Enzime Linked Imunosorbent Assay). Foram incluídos 90 indivíduos, divididos em três grupos: 1) 38 pacientes com RSCcPN, 2) 26 com RSCsPN e 3) 26 controles. Resultados: Quarenta e dois por cento dos pacientes com RSCcPN (16/38), assim como os com RSCsPN (11/26) apresentaram amostras positivas para biofilmes bacterianos, mas não observou essa positividade no grupo controle (0/26). A análise para bactérias intracelulares demonstrou a presença em 31,5% de pacientes com RSCcPN (12/38), 19,2% em RSCsPN (5/26) e 0% nos controles (0/26). No estudo por FISH, 58% dos pacientes com RSCcPN (18/31) apresentaram positividade para S. aureus intracelular, seguido de 54% nos com RSCsPN (13/24) e em nenhum caso dos 24 analisados do grupo controle. Na avaliação por ELISA, apenas um paciente com RSCcPN foi positivo para a presença de superantígenos estafilocócicos. A avaliação da associação de biofilme bacteriano na superfície mucosa à MEV com bactéria intracelular à MET e com S. aureus intracelular por FISH nos dois diferentes grupos de RSC com e sem pólipo nasal, não mostrou diferença estatisticamente significativa. Conclusão: Foi observada uma maior prevalêcia de biofilmes e bactérias intracelulares em indivíduos com RSC com ou sem pólipo nasal, comparado a Resumo controles. Não houve diferença significativa dentre os grupos de RSC, com e sem pólipo nasal para a presença de biofilmes e bactérias intracelulares. Não houve associação entre a presença de biofilme e bactéria intracelular em pacientes com RSC. Os achados do presente estudo indicam que tanto biofilmes na superfície mucosa quanto microrganismos intracelulares podem estar envolvidos na fisiopatogenia da RSC. / Introduction: Although the pathophysiology of chronic rhinosinusitis (CRS) has not yet been fully elucidated, due to its heterogeneity and multifactorial etiology, there is a growing body of evidence that bacteria play a significant role in the genesis or perpetuation of chronic inflammation. One of the possible forms of acting are bacterial biofilms, which are commonly found in patients with CRS, and are associated with poor clinical outcomes in these patients. In addition to biofilms, there are some evidence pointing out that some bacterial species, especially Staphylococcus aureus (S. aureus), are able to invade into epithelial cells and remain viable intracellulary. Finally, it has been demonstrated that patients with CRS with nasal polyps (CRSwNP) have a high association with the presence of staphylococcal superantigens in the respiratory mucosa, responsible for the stimulation of marked local inflammatory responses. Although these different bacterial forms are well described in CRS, it is still unclear how they are associated in these individuals. Objectives: To evaluate the correlation between the presence of biofilms, intracellular bacteria expression and S. aureus superantigens in CRS patients (with and without nasal polyposis) compared to a control group. Casuistic and Methods: We evaluated the prevalence of bacterial biofilms, intracellular bacteria and the presence of bacterial superantigens in individuals with CRSwNP, without nasal polyp (CRSsNP) and controls, evaluating the association of prevalence distribution of these different groups (Fisher exact test, level of significance set at p<0.05). The biofilms were defined by morphological characteristics by scanning electron microscopy, intracellular bacteria were analyzed by transmission electron microscopy and fluorescence in situ hybridization (FISH) for S. aureus, and S. aureus A-E superantigens were quantified by ELISA. Ninety individuals were included, divided into 38 patients with CRSwNP, 26 patients with CRSsNP and 26 control patients. Results: 42% of patients with CRSwNP (16/38) as well as those with CRSsNP (11/26) presented positive samples for bacterial biofilms, while none of the control patients (0/26) had positive samples. The analysis for intracellular bacteria showed the presence in 31.5% of patients with CRSwNP (12/38), 19.2% in CRSsNP (5/26) and 0% in control patients (0/26). In the FISH study, 58% of patients with CRSwNP (18/31) presented intracellular S. aureus positivity, followed by 54% in patients with CRSsNP (13/24) and in none of the 24 analyzed in the control group. In the ELISA evaluation, only one patient with CRSwNP was positive for the presence of staphylococcal superantigens. The evaluation of the association of bacterial biofilm on the mucosal surface (SEM) with intracellular bacteria (MET) and with intracellular S. aureus by FISH in the two different groups of CRS (with and without nasal polyps) did not show a statistically significant difference. Conclusion: We found a higher prevalence of biofilms and intracellular bacteria in individuals with CRS, either with and without nasal polyps. There was no significant difference between the groups of CRS, with and without nasal polyp, for the presence of biofilms or intracellular bacteria. There was no significant diference on the association of biofilms and intracellular bacteria on pacientes with CRS. Our data indicate that both biofilms on the mucosal surface and intracellular microorganisms may be involved in the pathophysiology of CRS.

L’interrogation efficace d’images en utilisant un système de recherche d’image est un problème qui a attiré l’attention de la communauté de recherche depuis une longue période. Dans le domaine médical, les images sont de plus en plus produites en grandes quantités en raison de leur intérêt croissant pour de nombreuses pratiques médicales comme le diagnostic, la rédaction de rapports et l’enseignement. Cette thèse propose un système d’annotation et recherche sémantique d’images gastroentérologiques basé sur une nouvelle ontologie des polypes qui peut être utilisée pour aider les médecins à décider comment traiter un polype. La solution proposée utilise une ontologie de polype et se base sur une adaptation des raisonnements standard des logiques de description pour permettre une construction semi-automatique de requêtes et d’annotation d’images. Une deuxième contribution de ce travail consiste dans la proposition d’une nouvelle approche pour le calcul de réponses relaxées des requêtes ontologiques basée sur une notion de distance entre un individu donné et une requête donnée. Cette distance est calculée en comptant le nombre d’opérations élémentaires à appliquer à une ABox afin de rendre un individu donné x, une réponse correcte à une requête. Ces opérations élémentaires sont l’ajout à ou la suppression d’une ABox, d’assertions sur des concepts atomiques (ou leur négation) et/ou des rôles atomiques. La thèse propose plusieurs sémantiques formelles pour la relaxation de requêtes et étudie les problèmes de décision et d’optimisation sous-jacents. / Querying efficiently images using an image retrieval system is a long standing and challenging research problem.In the medical domain, images are increasingly produced in large quantities due their increasing interests for many medical practices such as diagnosis, report writing and teaching. This thesis proposes a semantic-based gastroenterological images annotation and retrieval system based on a new polyp ontology that can be used to support physicians to decide how to deal with a polyp. The proposed solution uses a polyp ontology and rests on an adaptation of standard reasonings in description logic to enable semi automatic construction of queries and image annotation.A second contribution of this work lies in the proposition of a new approach for computing relaxed answers of ontological queries based on a notion of an edit distance of a given individual w.r.t. a given query. Such a distance is computed by counting the number of elementary operations needed to be applied to an ABox in order to make a given individual a correct answer to a given query. The considered elementary operations are adding to or removing from an ABox, assertions on atomic concept, a negation of an atomic concept or an atomic role. The thesis proposes several formal semantics for such query approximation and investigates the underlying decision and optimisation problems.

abstract: Colorectal cancer is the second-highest cause of cancer-related deaths in the United States with approximately 50,000 estimated deaths in 2015. The advanced stages of colorectal cancer has a poor five-year survival rate of 10%, whereas the diagnosis in early stages of development has showed a more favorable five-year survival rate of 90%. Early diagnosis of colorectal cancer is achievable if colorectal polyps, a possible precursor to cancer, are detected and removed before developing into malignancy. The preferred method for polyp detection and removal is optical colonoscopy. A colonoscopic procedure consists of two phases: (1) insertion phase during which a flexible endoscope (a flexible tube with a tiny video camera at the tip) is advanced via the anus and then gradually to the end of the colon--called the cecum, and (2) withdrawal phase during which the endoscope is gradually withdrawn while colonoscopists examine the colon wall to find and remove polyps. Colonoscopy is an effective procedure and has led to a significant decline in the incidence and mortality of colon cancer. However, despite many screening and therapeutic advantages, 1 out of every 4 polyps and 1 out of 13 colon cancers are missed during colonoscopy. There are many factors that contribute to missed polyps and cancers including poor colon preparation, inadequate navigational skills, and fatigue. Poor colon preparation results in a substantial portion of colon covered with fecal content, hindering a careful examination of the colon. Inadequate navigational skills can prevent a colonoscopist from examining hard-to-reach regions of the colon that may contain a polyp. Fatigue can manifest itself in the performance of a colonoscopist by decreasing diligence and vigilance during procedures. Lack of vigilance may prevent a colonoscopist from detecting the polyps that briefly appear in the colonoscopy videos. Lack of diligence may result in hasty examination of the colon that is likely to miss polyps and lesions. To reduce polyp and cancer miss rates, this research presents a quality assurance system with 3 components. The first component is an automatic polyp detection system that highlights the regions with suspected polyps in colonoscopy videos. The goal is to encourage more vigilance during procedures. The suggested polyp detection system consists of several novel modules: (1) a new patch descriptor that characterizes image appearance around boundaries more accurately and more efficiently than widely-used patch descriptors such HoG, LBP, and Daisy; (2) A 2-stage classification framework that is able to enhance low level image features prior to classification. Unlike the traditional way of image classification where a single patch undergoes the processing pipeline, our system fuses the information extracted from a pair of patches for more accurate edge classification; (3) a new vote accumulation scheme that robustly localizes objects with curvy boundaries in fragmented edge maps. Our voting scheme produces a probabilistic output for each polyp candidate but unlike the existing methods (e.g., Hough transform) does not require any predefined parametric model of the object of interest; (4) and a unique three-way image representation coupled with convolutional neural networks (CNNs) for classifying the polyp candidates. Our image representation efficiently captures a variety of features such as color, texture, shape, and temporal information and significantly improves the performance of the subsequent CNNs for candidate classification. This contrasts with the exiting methods that mainly rely on a subset of the above image features for polyp detection. Furthermore, this research is the first to investigate the use of CNNs for polyp detection in colonoscopy videos. The second component of our quality assurance system is an automatic image quality assessment for colonoscopy. The goal is to encourage more diligence during procedures by warning against hasty and low quality colon examination. We detect a low quality colon examination by identifying a number of consecutive non-informative frames in videos. We base our methodology for detecting non-informative frames on two key observations: (1) non-informative frames most often show an unrecognizable scene with few details and blurry edges and thus their information can be locally compressed in a few Discrete Cosine Transform (DCT) coefficients; however, informative images include much more details and their information content cannot be summarized by a small subset of DCT coefficients; (2) information content is spread all over the image in the case of informative frames, whereas in non-informative frames, depending on image artifacts and degradation factors, details may appear in only a few regions. We use the former observation in designing our global features and the latter in designing our local image features. We demonstrated that the suggested new features are superior to the existing features based on wavelet and Fourier transforms. The third component of our quality assurance system is a 3D visualization system. The goal is to provide colonoscopists with feedback about the regions of the colon that have remained unexamined during colonoscopy, thereby helping them improve their navigational skills. The suggested system is based on a new 3D reconstruction algorithm that combines depth and position information for 3D reconstruction. We propose to use a depth camera and a tracking sensor to obtain depth and position information. Our system contrasts with the existing works where the depth and position information are unreliably estimated from the colonoscopy frames. We conducted a use case experiment, demonstrating that the suggested 3D visualization system can determine the unseen regions of the navigated environment. However, due to technology limitations, we were not able to evaluate our 3D visualization system using a phantom model of the colon. / Dissertation/Thesis / Doctoral Dissertation Biomedical Informatics 2015

Introdução: Embora a fisiopatogenia da rinossinusite crônica (RSC) ainda não esteja totalmente elucidada, em virtude da sua heterogeneidade e multifatorialidade, existe um crescente corpo de evidências apontando que as bactérias exerçam um papel significativo na gênese ou perpetuação da inflamação crônica. Uma das possíveis formas de atuação são os biofilmes bacterianos, comumente encontrados em pacientes com RSC e que estão relacionados com má evolução clínica. Ainda, existem evidências de que algumas espécies bacterianas, especialmente o Staphylococcus aureus (S. aureus), são capazes de invadir as células epiteliais e permanecerem viáveis em seu interior. Por fim, tem se demonstrado que pacientes RSC com pólipo nasal (RSCcPN) revelam alta associação com a presença de superantígenos estafilocócicos na mucosa respiratória, responsáveis pela estimulação acentuada de respostas inflamatórias locais. Apesar de essas diferentes formas bacterianas estarem bem descritas na RSC, não se sabe ainda com clareza como elas estão associadas nesses indivíduos. Objetivos: Avaliar a associação entre a presença de biofilmes, bactérias intracelulares e superantígenos estafilocócicos em pacientes com RSC (com e sem pólipo nasal), comparados com o grupo controle. Casuística e Métodos: Avaliou-se a prevalência de biofilmes bacterianos, bactérias intracelulares e presença de superantígenos bacterianos em indivíduos com RSCcPN, sem pólipo nasal (RSCsPN) e controles, analisando a associação de distribuição de prevalência desses diferentes grupos (teste exato de Fisher, nível de significância quando p<0,05). Os biofilmes foram definidos por características morfológicas à microscopia eletrônica de varredura (MEV), as bactérias intracelulares foram analisadas por microscopia eletrônica de transmissão (MET) e hibridização fluorescente in situ (FISH) para S. aureus, e superantígenos de S. aureus A-E foram quantificados pela técnica de ELISA (Enzime Linked Imunosorbent Assay). Foram incluídos 90 indivíduos, divididos em três grupos: 1) 38 pacientes com RSCcPN, 2) 26 com RSCsPN e 3) 26 controles. Resultados: Quarenta e dois por cento dos pacientes com RSCcPN (16/38), assim como os com RSCsPN (11/26) apresentaram amostras positivas para biofilmes bacterianos, mas não observou essa positividade no grupo controle (0/26). A análise para bactérias intracelulares demonstrou a presença em 31,5% de pacientes com RSCcPN (12/38), 19,2% em RSCsPN (5/26) e 0% nos controles (0/26). No estudo por FISH, 58% dos pacientes com RSCcPN (18/31) apresentaram positividade para S. aureus intracelular, seguido de 54% nos com RSCsPN (13/24) e em nenhum caso dos 24 analisados do grupo controle. Na avaliação por ELISA, apenas um paciente com RSCcPN foi positivo para a presença de superantígenos estafilocócicos. A avaliação da associação de biofilme bacteriano na superfície mucosa à MEV com bactéria intracelular à MET e com S. aureus intracelular por FISH nos dois diferentes grupos de RSC com e sem pólipo nasal, não mostrou diferença estatisticamente significativa. Conclusão: Foi observada uma maior prevalêcia de biofilmes e bactérias intracelulares em indivíduos com RSC com ou sem pólipo nasal, comparado a Resumo controles. Não houve diferença significativa dentre os grupos de RSC, com e sem pólipo nasal para a presença de biofilmes e bactérias intracelulares. Não houve associação entre a presença de biofilme e bactéria intracelular em pacientes com RSC. Os achados do presente estudo indicam que tanto biofilmes na superfície mucosa quanto microrganismos intracelulares podem estar envolvidos na fisiopatogenia da RSC. / Introduction: Although the pathophysiology of chronic rhinosinusitis (CRS) has not yet been fully elucidated, due to its heterogeneity and multifactorial etiology, there is a growing body of evidence that bacteria play a significant role in the genesis or perpetuation of chronic inflammation. One of the possible forms of acting are bacterial biofilms, which are commonly found in patients with CRS, and are associated with poor clinical outcomes in these patients. In addition to biofilms, there are some evidence pointing out that some bacterial species, especially Staphylococcus aureus (S. aureus), are able to invade into epithelial cells and remain viable intracellulary. Finally, it has been demonstrated that patients with CRS with nasal polyps (CRSwNP) have a high association with the presence of staphylococcal superantigens in the respiratory mucosa, responsible for the stimulation of marked local inflammatory responses. Although these different bacterial forms are well described in CRS, it is still unclear how they are associated in these individuals. Objectives: To evaluate the correlation between the presence of biofilms, intracellular bacteria expression and S. aureus superantigens in CRS patients (with and without nasal polyposis) compared to a control group. Casuistic and Methods: We evaluated the prevalence of bacterial biofilms, intracellular bacteria and the presence of bacterial superantigens in individuals with CRSwNP, without nasal polyp (CRSsNP) and controls, evaluating the association of prevalence distribution of these different groups (Fisher exact test, level of significance set at p<0.05). The biofilms were defined by morphological characteristics by scanning electron microscopy, intracellular bacteria were analyzed by transmission electron microscopy and fluorescence in situ hybridization (FISH) for S. aureus, and S. aureus A-E superantigens were quantified by ELISA. Ninety individuals were included, divided into 38 patients with CRSwNP, 26 patients with CRSsNP and 26 control patients. Results: 42% of patients with CRSwNP (16/38) as well as those with CRSsNP (11/26) presented positive samples for bacterial biofilms, while none of the control patients (0/26) had positive samples. The analysis for intracellular bacteria showed the presence in 31.5% of patients with CRSwNP (12/38), 19.2% in CRSsNP (5/26) and 0% in control patients (0/26). In the FISH study, 58% of patients with CRSwNP (18/31) presented intracellular S. aureus positivity, followed by 54% in patients with CRSsNP (13/24) and in none of the 24 analyzed in the control group. In the ELISA evaluation, only one patient with CRSwNP was positive for the presence of staphylococcal superantigens. The evaluation of the association of bacterial biofilm on the mucosal surface (SEM) with intracellular bacteria (MET) and with intracellular S. aureus by FISH in the two different groups of CRS (with and without nasal polyps) did not show a statistically significant difference. Conclusion: We found a higher prevalence of biofilms and intracellular bacteria in individuals with CRS, either with and without nasal polyps. There was no significant difference between the groups of CRS, with and without nasal polyp, for the presence of biofilms or intracellular bacteria. There was no significant diference on the association of biofilms and intracellular bacteria on pacientes with CRS. Our data indicate that both biofilms on the mucosal surface and intracellular microorganisms may be involved in the pathophysiology of CRS.