Prognostic prediction models using Self-Attention for ICU patients developing acute kidney injury

Tese de mestrado, Ciência de Dados, Universidade de Lisboa, Faculdade de Ciências, 2022The general growth and improved accessibility to electronic health records demands an identical level of progress in terms of the research community regarding clinical models. The usage of machine learning techniques is key to this development, and so they are increasingly being used in large medical databases with the purpose of creating solutions that work for specified patients, no matter the task or the disease. Acute kidney injury (AKI) is a broad disease defined by abrupt changes in renal function. AKI has a high morbidity and mortality, with an increased focus on critically ill patients. The main goal of this thesis is to study the development of AKI within a patient’s stay in the intensive care unit (ICU). Data from the MIMIC-III database was used to collect information regarding the patients. After a detailed exclusion criteria, those were evaluated in terms of AKI stages, with the purpose of predicting the next value of AKI stage one hour after the sequence of information fed to the model. This can suggest the capacity of the model at predicting the aggravation of a patient’s AKI condition. The sequences used have hourly information for every feature, and were used sequences of 6h, 12h and 24h length. Self-attention mechanisms were used to make the predictions, using an adaptation for multi-variate time series built from the successfully used models on natural language processing (NLP) tasks. The predictions on this work were made for two variations of the KDIGO classification system: one where only the serum creatinine (SCr) criteria was taken into account to determine the patient’s AKI stage, and other where both SCr and urine output (UO) were considered. While most works addressing AKI only tend to use SCr values to determine the patient’s AKI condition, the results were compared using both approaches and were better when using both SCr and UO. For those experiments, the model achieved up to 68.05% accuracy predicting an episode of AKI, compared to the 66.67% accuracy achieved using only SCr values, which outperformed state-of-the-art results for both cases. Feature importance was also used for each dataset associated with the two variations of KDIGO classification system to identify what were the most important features. Furthermore, final results were compared when using all features versus only using the most 10 important ones

Development of alternative diet for the mass culture of the European cuttlefish Sepia officinalis

O objectivo desta dissertação era o desenvolvimento de dietas económicas que permitissem o cultivo em grande escala do choco, Sepia oficinalis. Esta foi dividida em duas grandes áreas de investigação, referentes aos hábitos alimentares das diversas fases da vida do choco, associados ao tamanho e à idade. A primeira parte focou os aspectos de cultivo de misidáceos para alimentar os juvenis de choco. A segunda parte consistiu em determinar os efeitos de dietas artificiais (em substituição de dietas naturais como camarão ou peixe congelado) no cultivo do choco, e determinar se estas poderiam substituir com sucesso as dietas naturais que são normalmente utilizadas.The objective of this dissertation research was to enable the mass culture of Sepia ofitcinalis through the development of inexpensive diets. It was divided into two major areas concerning the feeding habits of S. officinalis according to their age and size. The first part focused on the culture of mysids to feed hatchling cuttlefish. The second part consisted on testing the effects of artificial surimi diets fed to cuttlefish and deterrnine if they could successfully replace natural food (frozen shrimp or fish) that are nonnally used

Empirical Research of the ISO 9001:2015 Transition Process in Portugal: Motivations, Benefits, and Success Factors

An empirical study of more than 300 Portuguese organisations ISO 9001 certified, or in certification process, encompassing a wide range of activities sectors, was carried out. As of May 2017, 19% of the respondents already have ISO 9001:2015 certification and all the remaining one’s plan to complete the process in time. The principal reported benefits are risk-based thinking, mapping of the organisational context, and stakeholder identification. Simultaneously those were the issues that required more attention and effort to be mastered and implemented. Additionally, there is evidence that ISO 9001:2015 enhances both internal and external organisational issues and generates benefits for all the researched dimensions. Based on the respondents’ responses, organisations who claimed that external motivations were the primary drivers to ISO 9001:2015 implementation systematically rate higher all the benefits when compared with the rating ascribed by those organisations who claimed internal motivations. Moreover, it is possible to conclude that the perceived benefits from ISO 9001:2015 implementation and certification seem to be strongly influenced by two primary dimensions: the (smaller) organisation size and the (lesser) international presence.The authors would like to acknowledge the contribution of the respondents. CIDEM Centro de Investigação e Desenvolvimento em Engenharia Mecânica R&D unit is funded by the FCT – Portuguese Foundation for the Development of Science and Technology, Ministry of Science, Technology, and Higher Education, under the Project UID/EMS/0615/2016. This study had the financial support of FCT Fundação para a Ciência e Tecnologia of Portugal under the project UID/CEC/00319/2013. Pedro Domingues is supported by FCT Post-Doc Grant Reference SFRH/BPD/103322/2014.info:eu-repo/semantics/publishedVersio

Uma perspectiva geral sobre miocardites

A Miocardite é uma doença inflamatória do miocárdio com um espectro variado de apresentações clínicas que variam desde as mais subtis às mais complexas. É diagnosticada por critérios histológicos, imunológicos e imunoquímicos estabelecidos. É descrita como “um infiltrado inflamatório do miocárdio com necrose e/ou degeneração dos miócitos adjacentes”. Usualmente manifesta-se em pessoas aparentemente saudáveis e pode resultar em insuficiência cardíaca rapidamente progressiva (e muitas vezes fatal) e arritmia. A sua incidência é difícil de estimar devido à sua grande variedade de apresentações. A miocardite acomete preferencialmente indivíduos do sexo masculino em escalões etários jovens. A Miocardite é causada por uma grande variedade de organismos infecciosos, desordens autoimunes e agentes exógenos tendo também alguma predisposição genética e ambiental. As lesões ocorrem por efeito citotóxico directo do agente causal, resposta imune secundária causada pelo agente infeccioso, expressão de citocinas no miocárdio e indução aberrante da apoptose. Para fazer o seu diagnóstico existem vários métodos invasivos e não invasivos. Alguns ainda estão pouco desenvolvidos e carecem de validação. No entanto, o gold standard para o diagnóstico de miocardite é a biópsia endomiocárdica, apesar de apresentar alguns riscos. As guidelines para o tratamento da miocardite incluem diuréticos, inibidores da enzima de conversão da angiotensina ou antagonistas dos receptores de angiotensina e bloqueadores beta-adrenérgicos. Alguns estudos ainda estão a verificar a possibilidade de se recorrer a terapia antiviral e imunossupressora. Deve-se também aconselhar sobre modificações do estilo de vida, incluindo a redução de sódio da dieta, restrição de fluidos e evicção do uso de fármacos anti-inflamatórios não esteróides Os doentes com doença fulminante possuem um melhor prognóstico. A persistência do agente causal e a consequente inflamação crónica piora o prognóstico. Investigações futuras devem basear-se na tentativa de encontrar métodos diagnósticos não invasivos mais sensíveis e específicos de modo a melhorar o diagnóstico evitando os riscos de alguns métodos vigentes.Myocarditis is an inflammatory disease of the myocardium with a wide spectrum of presentations ranging from the subtle to the most complex. It is diagnosed by established histological, immunological and immunochemical criteria. It is described as “an inflammatory infiltrate of the myocardium with necrosis and/or degeneration of the adjacent myocites”. It usually manifests in apparently healthy people and may result in rapidly progressive heart failure (sometimes fatal) and arrhythmia. Its incidence is hard to estimate due to its wide variety of presentations. Myocarditis affects mainly males in younger age groups. The Myocarditis is caused by a variety of infectious organisms, autoimmune disorders and exogenous agents and also have some genetic predisposition and environmental. The lesions occur by direct cytotoxic effect of the causative agent, secondary immune response caused by the infectious agent, cytokine expression in the myocardium and aberrant induction of apoptosis. To make the diagnosis there are several invasive and noninvasive studies. Some are still underdeveloped and lack of validation. However, the gold standard for diagnosis of myocarditis is endomyocardial biopsy, despite some risks. The guidelines for the treatment of myocarditis include diuretics, angiotensin-converting enzyme inhibitors or angiotensin receptor antagonists and beta blockers. Some studies are still checking the possibility of using antiviral and immunosuppressive therapies. Patients should be advised on lifestyle changes, including reducing sodium intake, fluid restriction and avoidance of the use of nonsteroidal anti-inflammatory drugs. Patients with fulminant disease have a better prognosis. The persistence of the causative agent and the resulting chronic inflammation worsens the prognosis. Further investigations should be based on trying to find noninvasive diagnostic methods with higher sensitivity and specificity in order to improve the diagnosis avoiding the risks of some existing methods

Mapping the sustainable development goals relationships

Sustainable development addresses humanity’s aspiration for a better life while observing the limitations imposed by nature. In 2015, the United Nations General Assembly approved the 17 Sustainable Development Goals (SDGs) with the aim to foster the organizational operationalization and integration of sustainability and, therefore, to address the current and forthcoming stakeholder needs and ensure a better and sustainable future for all, balancing the economic, social, and environmental development. However, it is not entirely clear which are the mutual relationships among the 17 SDGs and this study aims to tackle this research gap. The results of the correlation confirm that Poverty elimination (SDG1) and Good health and well-being (SDG3) have synergetic relationships with most of the other goals. SDG7 (Affordable and clean energy) has significant relationships with other SDGs (e.g., SDG1 (No poverty), SDG2 (Zero hunger), SDG3 (Good health and well-being), SDG8 (Decent work and economic growth), SDG13 (Climate action)). However, there is a moderate negative correlation with SDG12 (Responsible consumption and production), which emphasizes the need to improve energy efficiency, increase the share of clean and renewable energies and improve sustainable consumption patterns worldwide. There is also confirmation that SDG12 (Responsible consumption and production) is the goal strongly associated with trade-offs. To sum up, this research suggests that change towards achieving the Sustainable Development Goals offers many opportunities for reinforcing rather than inhibiting itself. However, some SDGs show no significant correlation with other SDGs (e.g., SDG13 (Climate action) and SDG17 (Partnerships for the goals), which highlights the need for future research.CIDEM: R&D unit is funded by the FCT—Portuguese Foundation for the Development of Science and Technology, Ministry of Science, Technology, and Higher Education, under the Project UID/EMS/0615/2019. Pedro Domingues (ALGORITMI Research Centre) benefited from financial support by FCT–Fundação para a Ciência e Tecnologia within the R&D Units Project Scope: UIDB/00319/2020

Engineering Saccharomyces cerevisiae for the production of sugaralcohols

Excess sugar intake contributes to weight gain, obesity, and related diseases [1]. Considering the growing demand for healthier products, most food manufacturers are focused on the reformulation of foods and beverages to reduce added sugar, using natural sweeteners and combinations of these ingredients. Arabitol is a sugar alcohol presenting similar properties to its isomer xylitol, a well-established sugar substitute [2]. The microbiological production of these sugar alcohols has received growing interest as an alternative to the expensive chemical synthesis that involves negative environmental effects. The yeast Saccharomyces cerevisiae considered a platform cell factory for sustainable biorefineries [3], encodes in its genome an NADPH-dependent aldose reductase that converts aldoses into their corresponding alcohols [4]. Taking advantage of its broad substrate specificity, we demonstrate the feasibility of using an engineered industrial yeast strain for the simultaneous conversion of arabinose and xylose to arabitol and xylitol. In addition, the recombinant strain was further engineered to improve arabinose transport capacity, improving the arabinose to arabitol conversion yield. This strategy for the simultaneous production of sugar alcohols is a step forward in the development of a multi-chemical yeast production platform capable to convert bulk sugars present in agro-food residues, contributing to the establishment of a bioeconomy.This study was supported by the Portuguese Foundation for Science and Technology (FCT) - UID/BIO/04469/2020 unit; Ph.D grant SFRH/BD/132717/2017 to Sara L. Baptista and Ph.D. grant SFRH/BD/146367/2019 to Pedro O. Soares This study was also supported by BioVino project (0688_BIOVINO_6_E), funded by INTERREG España - Portugal and European Regionalinfo:eu-repo/semantics/publishedVersio

Flood Risk Assessment in the Lisbon Metropolitan Area

Flood processes are one of the most challenging to risk assessment and management. In many situations, peak flows are generated kilometers away from the places where inundation is observed. Scale in flood risk assessments is a fundamental factor when estimating hazard, exposure, and vulnerability. Municipal, civil parish, and building-level information are used to construct flood risk indexes and profiles. It is observed that, depending on the scale at which it is represented, the same root information provides distinct insights into flood risk expression in the Lisbon Metropolitan Area. When compared with the Flood Directive critical areas, the results show they are mostly consistent with the results at the different scales, identifying the same hotspots of flood risk (in the Loures, V. F. Xira, and Setúbal municipalities) as those selected during the Directive’s implementation. Flood loss reduction implies the involvement of distinct risk practitioners and decision-makers, acting at distinct scales and sectors related to risk governance. Interconnections between flood risk components and between flood processes and other potential cascading processes are still insufficiently known and require the priority of society.info:eu-repo/semantics/publishedVersio

Effects of different prey and rearing densities on growth and survival of octopus maya hatchlings

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