Computer-aided Visualization of Colonoscopy

Colonoscopy is the most widely used medical technique to examine the human large intestine (colon) and eliminate precancerous or malignant lesions, i.e., polyps. It uses a high-definition camera to examine the inner surface of the colon. Very often, a portion of the colon surface is not visualized during the procedure. Unsurveyed portions of the colon can harbor polyps that then progress to colorectal cancer. Unfortunately, it is hard for the endoscopist to realize there is unsurveyed surface from the video as it is formed. A system to alert endoscopists to missed surface area could thus more fully protect patients from colorectal cancer following colonoscopy. In this dissertation computer-aided visualization techniques were developed in order to solve this problem:1. A novel Simultaneous Localization and Mapping (SLAM) algorithm called RNNSLAM was proposed to address the difficulties of applying a traditional SLAM system on colonic images. I improved a standard SLAM system with a previously proposed Recurrent Neural Network for Depth and Pose Estimation (RNN-DP). The combination of SLAM’s optimization mechanism and RNN-DP’s prior knowledge achieved state-of-the-art performance on colonoscopy, especially addressing the drift problem in both SLAM and RNN-DP. A fusion module was added to this system to generate a dense 3D surface.2. I conducted exploration research on recognizing colonic places that have been visited based on video frames. This technique called image relocalization or retrieval is needed for helping the endoscopist to fully survey the previously unsurveyed regions. A benchmark testing dataset was created for colon image retrieval. Deep neural networks were successfully trained using Structure from Motion results on colonoscopy and achieved promising results.3. To visualize highly-curved portions of a colon or the whole colon, a generalized cylinder deformation algorithm was proposed to semi-flatten the geometry of the colon model for more succinct and global visualization.Doctor of Philosoph

Registration of prone and supine CT colonography images and its clinical application

Computed tomographic (CT) colonography is a technique for detecting bowel cancer and potentially precancerous polyps. CT imaging is performed on the cleansed and insufflated bowel in order to produce a virtual endoluminal representation similar to optical colonoscopy. Because fluids and stool can mimic pathology, images are acquired with the patient in both prone and supine positions. Radiologists then match endoluminal locations visually between the two acquisitions in order to determine whether pathology is real or not. This process is hindered by the fact that the colon can undergo considerable deformation between acquisitions. Robust and accurate automated registration between prone and supine data acquisitions is therefore pivotal for medical interpretation, but a challenging problem. The method proposed in this thesis reduces the complexity of the registration task of aligning the prone and supine CT colonography acquisitions. This is done by utilising cylindrical representations of the colonic surface which reflect the colon's specific anatomy. Automated alignment in the cylindrical domain is achieved by non-rigid image registration using surface curvatures, applicable even when cases exhibit local luminal collapses. It is furthermore shown that landmark matches for initialisation improve the registration's accuracy and robustness. Additional performance improvements are achieved by symmetric and inverse-consistent registration and iteratively deforming the surface in order to compensate for differences in distension and bowel preparation. Manually identified reference points in human data and fiducial markers in a porcine phantom are used to validate the registration accuracy. The potential clinical impact of the method has been evaluated using data that reflects clinical practise. Furthermore, correspondence between follow-up CT colonography acquisitions is established in order to facilitate the clinical need to investigate polyp growth over time. Accurate registration has the potential to both improve the diagnostic process and decrease the radiologist's interpretation time. Furthermore, its result could be integrated into algorithms for improved computer-aided detection of colonic polyps

EXAMINING PROTEIN CONFORMATIONAL DYNAMICS USING COMPUTATIONAL TECHNIQUES: STUDIES ON PHOSPHATIDYLINOSITOL-3-KINASE AND THE SODIUM-IODIDE SYMPORTER

Experimental biophysics techniques used to study proteins, polymers of amino acids that comprise most therapeutic targets of human disease, face limitations in their ability to interrogate the continual structural fluctuations exhibited by these macromolecules in the context of their myriad cellular functions. This dissertation aims to illustrate case studies that demonstrate how protein conformational dynamics can be characterized using computational methods, yielding novel insights into their functional regulation and activity. Towards this end, the work presented here describes two specific membrane proteins of therapeutic relevance: Phosphoinositide 3-kinase (PI3Kα), and the Na+/I- symporter (NIS). The PI3KCA gene, encoding the catalytic subunit of the PI3Kα protein that phosphorylates phosphatidylinositol-4,5-bisphosphate (PIP2) to generate phosphatidylinositol-3,4,5-triphosphate (PIP3), is highly mutated in human cancer. As such, a deeper mechanistic understanding of PI3Kα could facilitate the development of novel chemotherapeutic approaches. The second chapter of this dissertation describes molecular dynamics (MD) simulations that were conducted to determine how PI3Kα conformations are influenced by physiological effectors and the nSH2 domain of a regulatory subunit, p85. The results reported here suggest that dynamic allostery plays a role in populating the catalytically competent conformation of PI3Kα. NIS, a thirteen-helix transmembrane protein found in the thyroid and other tissues, transports iodide, a required constituent of thyroid hormones T3 and T4. Despite extensive experimental information and clinical data, many mechanistic details about NIS remain unresolved. The third chapter of this dissertation describes the results of unbiased and enhanced-sampling MD simulations of inwardly and outwardly open models of bound NIS under an enforced ion gradient. Simulations of NIS in the absence or presence of perchlorate are also described. The work presented in this dissertation aims to add to our mechanistic understanding of NIS ion transport and elucidate conformational states that occur between the inward and outward transitions of NIS in the absence and presence of bound Na+ and I- ions, which can provide valuable insight into its physiological activity and inform therapeutic interventions. Taken together, these case studies demonstrate the ability of computational techniques to provide novel insights into the impact of structural dynamics on the functional regulation of therapeutically important biological macromolecules

Using proteomic technologies to understand the impact of stress and nutritional factors on fish metabolism, welfare and quality

As the scale of aquacultural activities increases, we increasingly face challenges, not only in terms of sustainability, but also regarding issues like animal welfare and product quality. Within these research fields, proteomics (along with other -omics) is establishing itself as an invaluable tool for an untargeted assessment of the impact of exogenous stimuli on fish metabolism. This dissertation describes work developed in this area, where proteomic technologies were used to understand the impact of stress and nutritional factors on fish metabolism, welfare and quality. Gilthead seabream was chosen as the main biological model, due to its high importance in the Portuguese aquaculture sector, with Senegalese sole as secondary model. These studies were focused on both skeletal muscle and liver tissue. Results demonstrated that a reproducible proteomic analysis of the sarcoplasmic fraction of gilthead seabream muscle is feasible, with pre-slaughter stress inducing a clear hastening of the transition between the pre-rigor and post-rigor profiles. Comparatively, glycerol supplementation (as a tool to modulate muscle glycogen reserves) was shown to have a more subtle impact on the sarcoplasmic proteome of gilthead seabream, with results generally suggesting adaptive effects associated with this dietary factor. Hepatic proteome analyses revealed a high sensitivity towards both stress and dietary factors, with stress factors again displaying a broader impact on protein expression. In these experiments, the proteomic responses to sources of stress displayed specificities that depend on both the biological model and the type/duration of stressor, despite some degree of overlap in terms of the affected pathways. Concluding, despite the apparent resilience of gilthead seabream quality attributes in regards to nutritional and/or stress factors, proteome analysis revealed that these factors have an impact on both muscle and liver metabolism, being likely to affect post-mortem muscle degradation dynamics. The suggestion of specific candidates for further targeted studies underlines the usefulness of proteomics in this context.A aquacultura, apesar de se tratar de uma atividade humana que já conta com milénios de existência, entrou numa fase de crescimento surpreendente a partir da década de 60 do século passado, sendo que atualmente ultrapassa já o sector pesqueiro como principal fornecedor de produtos alimentares derivados de organismos aquáticos. Por outro lado, embora este crescimento prodigioso tenha acarretado mais-valias no que respeita ao custo e acessibilidade destes produtos alimentares (de elevada qualidade nutricional) às populações em geral, cada vez mais nos deparamos com diversos desafios, não só ao nível da sustentabilidade a longo-prazo destas atividades, como ao nível de questões relacionadas com o bem-estar animal e com a qualidade (nutricional e organolética) do produto final. Neste contexto, a proteómica (assim como a genómica, transcriptómica e metabolómica) tem-se estabelecido nos últimos anos como uma valiosa ferramenta na avaliação holística do impacto de fatores extrínsecos sobre os processos celulares dos peixes. O trabalho descrito nesta dissertação foca-se precisamente na aplicação de ferramentas proteómicas para o estudo do impacto do stress (a curto e a longo-prazo) no metabolismo dos peixes e processos de decomposição post-mortem (e, consequentemente, o seu efeito a nível do bem-estar dos peixes e da qualidade do produto final), assim como a interação de fatores nutricionais com estes fatores de stress. Para o efeito, procurou-se efetuar análises proteómicas ao nível de dois tecidos: por um lado, o músculo esquelético (i.e. o filete), dado que constitui a principal parte comestível do peixe; por outro, o fígado, que é o principal órgão responsável pelo controlo central dos processos metabólicos. Estes estudos foram realizados utilizando a dourada (Sparus aurata) como principal modelo animal, dada a sua importância no sector nacional de aquacultura. Para efeitos de comparação, foi ainda efetuado um estudo em linguado (Solea senegalensis), visto se tratar também de uma espécie relevante na aquacultura nacional e apresentar particular sensibilidade a fatores de stress, quando em cativeiro. No decorrer deste trabalho, foram realizados vários ensaios focados no tecido muscular da dourada, particularmente no que respeita a fatores imediatamente pre-mortem e o seu impacto nos processos de decomposição e, consequentemente, nas propriedades organoléticas do produto final. Os resultados obtidos confirmam a possibilidade de isolar a fração sarcoplasmática do proteoma muscular da dourada de forma reprodutível, dado que a sua aplicação aparentemente não aumenta a quantidade de ruído técnico inerente à análise do proteoma (Capítulo 2). A aplicação desta metodologia no estudo do stress pré-abate demonstrou um forte efeito deste tipo de stress pré-mortem no proteoma sarcoplasmático, claramente acelerando a transição entre um perfil pré-rigor e um perfil pós-rigor (Capítulo 3). Para além disso, apesar do impacto de fatores de stress sobre o proteoma muscular da dourada ser muito maior e mais abrangente do que o de fatores nutricionais, também se tornou claro que estes últimos (particularmente, o caso da suplementação alimentar com glicerol) podem induzir um efeito positivo ao nível das reservas de energia pré-mortem, podendo portanto constituir um fator mitigante no impacto dos efeitos de fatores de stress (Capítulo 4). Em relação aos ensaios focados na resposta proteómica do fígado face a fatores nutricionais e de stress, os resultados geralmente demonstram uma maior sensibilidade (comparado ao tecido muscular) face a estímulos externos, com os fatores de stress uma vez mais induzindo um maior impacto no proteoma comparativamente aos fatores nutricionais. Comparando os dois modelos animais utilizados (dourada e linguado), verificou-se que, apesar das semelhanças entre os dois modelos quando sujeitos a fatores de stress crónico em termos de vias metabólicas afetadas, existe uma fraca sobreposição em termos de proteínas especificamente afetadas, sugerindo a existência de idiossincrasias inerentes a cada espécie no que toca à sua resposta a fatores de stress (Capítulos 5 e 6). De facto, mesmo a aplicação de diferentes fatores de stress no mesmo modelo (dourada), em situações experimentais idênticas, demonstra a existência de uma dependência entre o tipo/duração do fator de stress aplicado e a resposta proteómica induzida, a nível hepático (Capítulo 5). Finalmente, conseguiu-se demonstrar que os dados obtidos por espectroscopia de infravermelho transmissiva do fígado de dourada fornecem importante informação que é tanto consistente como complementar à informação fornecida por metodologias proteómicas, providenciando um contributo significativo para o estudo do impacto do stress térmico sazonal no metabolismo da dourada, assim como para a formulação de dietas especiais fortificadas que providenciem um efeito positivo demonstrável no sentido de mitigar o impacto deste fator de stress (Capítulo 7). Concluindo, este trabalho demonstrou que tanto o stress crónico como o stress pré-abate induzem efeitos significativos a nível do proteoma muscular e hepático de peixes como a dourada e o linguado. É importante notar também que, em algumas das experiências, se demonstrou o potencial de fatores nutricionais na mitigação de alguns dos efeitos do stress induzido (tanto a nível hepático como a nível muscular). Para além disso, apesar da observação de claros efeitos induzidos por fatores nutricionais e de stress sobre o proteoma muscular, poucos efeitos foram notados em termos de impacto nas propriedades organoléticas do produto final (nomeadamente, textura, aroma e aspeto visual) que, apesar de positivo (dado ilustrar a robustez dos traços fenotípicos e propriedades organoléticas da dourada, face a fatores extrínsecos), torna difícil a utilização da dourada como modelo ótimo no estudo das relações entre o bem-estar animal e possíveis efeitos indesejados a nível da qualidade do produto final. Apesar disto, é inegável que estes fatores apresentam um impacto não-negligenciável sobre o bem-estar e o metabolismo dos peixes, facto atestado pelos resultados descritos nesta dissertação. Exemplos específicos de candidatos de estudo interessantes em futuros trabalhos nesta área incluem a proteína DJ-1, a proteína inibidora da Raf cinase (RKIP), a fosfohistidina fosfatase (PHP), entre outras proteínas regulatórias cuja expressão se demonstrou ser afetada por fatores nutricionais e de stress. Tudo isto demonstra a utilidade da proteómica no contexto da aquacultura, particularmente na área do bem-estar animal, como uma ferramenta sensível na deteção de sinais de stress fisiológico/celular e desvios metabólicos, mesmo quando estes não são aparentes mediante o recurso a técnicas clássicas.Universidade do Algarve, Faculdade de Ciências e Tecnologi

Unveiling the Molecular Mechanisms Regulating the Activation of the ErbB Family Receptors at Atomic Resolution through Molecular Modeling and Simulations

The EGFR/ErbB/HER family of kinases contains four homologous receptor tyrosine kinases that are important regulatory elements in key signaling pathways. To elucidate the atomistic mechanisms of dimerization-dependent activation in the ErbB family, we have performed molecular dynamics simulations of the intracellular kinase domains of the four members of the ErbB family (those with known kinase activity), namely EGFR, ErbB2 (HER2) and ErbB4 (HER4) as well as ErbB3 (HER3), an assumed pseudokinase, in different molecular contexts: monomer vs. dimer, wildtype vs. mutant. Using bioinformatics and fluctuation analyses of the molecular dynamics trajectories, we relate sequence similarities to correspondence of specific bond-interaction networks and collective dynamical modes. We find that in the active conformation of the ErbB kinases (except ErbB3), key subdomain motions are coordinated through conserved hydrophilic interactions: activating bond-networks consisting of hydrogen bonds and salt bridges. The inactive conformations also demonstrate conserved bonding patterns (albeit less extensive) that sequester key residues and disrupt the activating bond network. Both conformational states have distinct hydrophobic advantages through context-specific hydrophobic interactions. The inactive ErbB3 kinase domain also shows coordinated motions similar to the active conformations, in line with recent evidence that ErbB3 is a weakly active kinase, though the coordination seems to arise from hydrophobic interactions rather than hydrophilic ones. We show that the functional (activating) asymmetric kinase dimer interface forces a corresponding change in the hydrophobic and hydrophilic interactions that characterize the inactivating interaction network, resulting in motion of the αC-helix through allostery. Several of the clinically identified activating kinase mutations of EGFR act in a similar fashion to disrupt the inactivating interaction network. Our molecular dynamics study reveals the asymmetric dimer interface helps progress the ErbB family through the activation pathway using both hydrophilic and hydrophobic interaction. There is a fundamental difference in the sequence of events in EGFR activation compared with that described for the Src kinase Hck

Multiscale Biomechanics and Tribology of Inorganic and Organic Systems

This open access book gathers authoritative contributions concerning multiscale problems in biomechanics, geomechanics, materials science and tribology. It is written in memory of Sergey Grigorievich Psakhie to feature various aspects of his multifaceted research interests, ranging from theoretical physics, computer modeling of materials and material characterization at the atomic scale, to applications in space industry, medicine and geotectonics, and including organizational, psychological and philosophical aspects of scientific research and teaching as well. This book covers new advances relating to orthopedic implants, concerning the physiological, tribological and materials aspects of their behavior; medical and geological applications of permeable fluid-saturated materials; earthquake dynamics together with aspects relating to their managed and gentle release; lubrication, wear and material transfer in natural and artificial joints; material research in manufacturing processes; hard-soft matter interaction, including adhesive and capillary effects; using nanostructures for influencing living cells and for cancer treatment; manufacturing of surfaces with desired properties; self-organization of hierarchical structures during plastic deformation and thermal treatment; mechanics of composites and coatings; and many more. Covering established knowledge as well as new models and methods, this book provides readers with a comprehensive overview of the field, yet also with extensive details on each single topic