Automatic Reporting of TBI Lesion Location in CT based on Deep Learning and Atlas Mapping

Tese de mestrado integrado, Engenharia Biomédica e Biofísica (Biofísica Médica e Fisiologia de Sistemas), 2021, Universidade de Lisboa, Faculdade de CiênciasThe assessment of Computed Tomography (CT) scans for Traumatic Brain Injury (TBI) management remains a time consuming and challenging task for physicians. Computational methods for quantitative lesion segmentation and localisation may increase consistency in diagnosis and prognosis criteria. Our goal was to develop a registration-based tool to accurately localise several lesion classes (i.e., calculate the volume of lesion per brain region), as an extension of the Brain Lesion Analysis and Segmentation Tool for CT (BLAST-CT). Lesions were located by projecting a Magnetic Resonance Imaging (MRI) labelled atlas from the Montreal Neurological Institute (MNI MRI atlas) to a lesion map in native space. We created a CT template to work as an intermediate step between the two imaging spaces, using 182 non-lesioned CT scans and an unbiased iterative registration approach. We then non-linearly registered the parcellated atlas to the CT template, subsequently registering (affine) the result to native space. From the final atlas alignment, it was possible to calculate the volume of each lesion class per brain region. This pipeline was validated on a multi-centre dataset (n=839 scans), and defined three methods to flag any scans that presented sub-optimal results. The first one was based on the similarity metric of the registration of every scan to the study-specific CT template, the second aimed to identify any scans with regions that were completely collapsed post registration, and the final one identified scans with a significant volume of intra-ventricular haemorrhage outside of the ventricles. Additionally, an assessment of lesion prevalence and of the false negative and false positive rates of the algorithm, per anatomical region, was conducted, along with a bias assessment of the BLAST-CT tool. Our results show that the constructed pipeline is able to successfully localise TBI lesions across the whole brain, although without voxel-wise accuracy. We found the error rates calculated for each brain region to be inversely correlated with the lesion volume within that region. No considerable bias was identified on BLAST-CT, as all the significant correlation coefficients calculated between the Dice scores and clinical variables (i.e., age, Glasgow Coma Scale, Extended Glasgow Outcome Scale and Injury Severity Score) were below 0.2. Our results also suggest that the variation in DSC between male and female patients within a specific age range was caused by the discrepancy in lesion volume presented by the scans included in each sample

Regulation and function of the cell wall polymer lipoteichoic acid in staphylococcus aureus

A thesis submitted for the Degree of Master in Medical microbiologyExperimental work performed at the Centre for Molecular Bacteriology and Infection, Imperial College LondonLipoteichoic acid (LTA) is an important polymer present in the envelope of various Gram-positive bacteria. In Staphylococcus aureus it is composed of a polyglycerolphosphate chain synthesised by the enzyme LtaS, and is anchored to the membrane via a glycolipid anchor. Depletion of LTA is known to cause growth arrest, aberrant positioning of septa and enlargement of cells leading to eventual cell lysis. This highlights the importance of LTA for bacterial growth and also suggests a possible link between LTA synthesis and cell division. Although key enzymes required for LTA synthesis have been identified, how this process is regulated has not been elucidated. This study investigates the mechanisms of regulation of LTA synthesis, as well as provides further insights into the roles of LTA in S. aureus. In this study, nuclear magnetic resonance (NMR) was used to experimentally confirm a function for LTA in the incorporation of D-alanines into a second polymer, wall teichoic acid (WTA). LTA was also shown to be essential not only for bacterial growth, but also for bacterial survival, as cells become bactericidal in its absence. Furthermore, fluorescence microscopy using a GFP-tagged version of the synthase enzyme indicated that LtaS localises to the septum, suggesting a possible role for LTA in cell division. Regarding LTA regulation, this work has shown that the ltaS gene has two promoters and a large upstream UTR, but that only one promoter is essential and sufficient for expression. Studying the effect of salt stress on LTA production has also revealed that an increase the NaCl concentration in the media causes a reduction in the levels of LTA produced, which in turn has an effect on growth. However this is not due to a decrease in the levels of LtaS, reflecting a possible ionic or osmotic effect on LtaS enzymatic activity

Analysing race and sex bias in brain age prediction

Brain age prediction from MRI has become a popular imaging biomarker associated with a wide range of neuropathologies. The datasets used for training, however, are often skewed and imbalanced regarding demographics, potentially making brain age prediction models susceptible to bias. We analyse the commonly used ResNet-34 model by conducting a comprehensive subgroup performance analysis and feature inspection. The model is trained on 1,215 T1-weighted MRI scans from Cam-CAN and IXI, and tested on UK Biobank (n=42,786), split into six racial and biological sex subgroups. With the objective of comparing the performance between subgroups, measured by the absolute prediction error, we use a Kruskal-Wallis test followed by two post-hoc Conover-Iman tests to inspect bias across race and biological sex. To examine biases in the generated features, we use PCA for dimensionality reduction and employ two-sample Kolmogorov-Smirnov tests to identify distribution shifts among subgroups. Our results reveal statistically significant differences in predictive performance between Black and White, Black and Asian, and male and female subjects. Seven out of twelve pairwise comparisons show statistically significant differences in the feature distributions. Our findings call for further analysis of brain age prediction models.Comment: MICCAI Workshop on Fairness of AI in Medical Imaging (FAIMI 2023

A abordagem triangular como base do processo ensino-aprendizagem em artes visuais

Este relatório é o reflexo do trabalho desenvolvido nas Unidades Curriculares de Prática Profissional II (Educação Pré-Escolar) e Prática Profissional III (1º Ciclo) do curso de Mestrado em Educação Básica e Ensino do 1º Ciclo do Ensino Básico do Instituto Politécnico de Beja. Esta investigação baseada na prática centrou-se na questão da Planificação em Artes Visuais para o 1ºCiclo com recurso à abordagem triangular de Ana Mae Barbosa, e uma reflexão sobre a metodologia PBL (aprendizagem baseada num problema) como metodologia utilizada na exploração dos conteúdos científicos, na planificação das atividades à luz das Aprendizagens Essenciais e do Perfil do Aluno à saída da Escolaridade Obrigatória. Relacionou-se as Aprendizagens Essenciais para as Artes Visuais com a Abordagem Triangular de Ana Mae Barbosa ilustrando-se nas atividades planificadas e desenvolvidas ao longo do estágio e aplicadas a alunos do 3º ano de escolaridade. Concluímos com uma visão globalizante da pertinência da fruição no processo de produção e ensino-aprendizagem, contextualizada da planificação e introdução de conteúdos científicos em Artes Visuais

Competências empreendedoras em técnicos de reabilitação psicomotora no contexto profissional

Mestrado em Reabilitação PsicomotoraO principal objetivo que norteia esta tese refere-se à promoção de competências empreendedoras em técnicos de Reabilitação Psicomotora, no contexto profissional e, traduz-se na seguinte questão de investigação: Como melhorar as competências empreendedoras dos técnicos de Reabilitação Psicomotora em contexto profissional? De modo a concretizar o objetivo estipulado foram elaborados dois artigos, um concetual e outro empírico, tendo-se reunido informação de diversas fontes, através de diferentes métodos. Os resultados obtidos através do artigo concetual, a partir da análise do estado da arte nesta área, revelam que não foram encontrados quaisquer estudos que analisassem a temática do intraempreendedorismo e das competências empreendedoras nos técnicos de Reabilitação Psicomotora, apesar das suas evidentes vantagens. Iniciou-se, portanto, um processo de consciencialização sobre a importância de promover as competências empreendedoras nas instituições, como forma de melhorar o desempenho dos técnicos e, consequentemente, da própria instituição. No que concerne ao artigo empírico, tendo este por base a promoção de competências empreendedoras nos técnicos de Reabilitação Psicomotora em contexto profissional, foi elaborado um conjunto de boas práticas/estratégias, a partir da análise da literatura e do testemunho dos diretores das instituições, para promover as competências empreendedoras na instituição, proporcionando aos técnicos, uma melhoria do perfil de competências profissionais e da própria dinâmica institucional. Assim, os resultados evidenciam alguma variação na importância atribuída por cada diretor em relação ao que mais valorizam nos técnicos de Reabilitação Psicomotora, destacando-se como competência empreendedora mais relevante a um melhor desempenho destes técnicos, a competência empreendedora relacionamento, seguindo-se a oportunidade, organização e compromisso. Esta tese constitui-se como um pequeno passo na construção de uma sociedade empreendedora, pautada pela inovação e excelência dos serviços, onde o intraempreendedorismo e as competências empreendedoras são uma constante no quotidiano profissional dos técnicos

A fluorescent reporter for single cell analysis of gene expression in clostridium difficile

Genetically identical cells growing under homogeneous growth conditions often display cell-cell variation in gene expression. This variation stems from noise in gene expression and can be adaptive allowing for division of labor and bet-hedging strategies. In particular, for bacterial pathogens, the expression of phenotypes related to virulence can show cell-cell variation. Therefore, understanding virulence-related gene expression requires knowledge of gene expression patterns at the single cell level. We describe protocols for the use of fluorescence reporters for single cell analysis of gene expression in the human enteric pathogen Clostridium difficile, a strict anaerobe. The reporters are based on modified versions of the human DNA repair enzyme O ( 6)-alkylguanine-DNA alkyltransferase, called SNAP-tag and CLIP-tag. SNAP becomes covalently labeled upon reaction with O ( 6)-benzylguanine conjugated to a fluorophore, whereas CLIP is labeled by O ( 6)-benzylcytosine conjugates. SNAP and CLIP labeling is orthogonal allowing for dual labeling in the same cells. SNAP and CLIP cassettes optimized for C. difficile can be used for quantitative studies of gene expression at the single cell level. Both the SNAP and CLIP reporters can also be used for studies of protein subcellular localization in C. difficile.</p