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

Identification of Saccharomyces cerevisiae genes involved in the resistance to multiple stresses during Very-High-Gravity and lignocellulosic biomass industrial fermentations

Most of the current processes for bioethanol production are based on the use of Very-High-Gravity (VHG) technology and the processing of lignocellulosic biomass, limited by the high osmotic pressure and ethanol concentration in the fermentation medium, and by inhibitors resulting from biomass pre-treatments, respectively. Aiming the optimization of strains for industrial bioethanol production an integrated approach was undertaken to identify genes required for simultaneous yeast resistance to different fermentation-related stresses. The integration of previous chemogenomics data was used to identify eight genes whose expression confers simultaneous resistance to high concentrations of glucose, acetic acid and ethanol, chemical stresses relevant for VHG fermentations; and eleven genes conferring simultaneous resistance to different inhibitors present during lignocellulosic fermentations. The expression of BUD31 and HPR1 lead to the increase of both ethanol yield and fermentation rate, while PHO85, VRP1 and YGL024w expression is required for maximal ethanol production in VHG fermentations. Five genes, ERG2, PRS3, RAV1, RPB4 and VMA8 were found to contribute to the maintenance of cell viability in wheat straw hydrolysate and/or for maximal fermentation rate of this substrate [1]. Moreover, the yeast disruptome was screened for strains with increased susceptibility to inhibitory compounds present in an industrial lignocellulosic hydrolysate obtained from wheat straw. With this genome-wide analysis, 42 determinants of resistance to inhibitors were identified showing a high susceptibility phenotype compared to the parental strain. The identified genes stand as preferential targets for genetic engineering manipulation to generate more robust and efficient industrial strains

Identification of candidate genes for yeast engineering to improve bioethanol production in very high gravity and lignocellulosic biomass industrial fermentations

<p>Abstract</p> <p>Background</p> <p>The optimization of industrial bioethanol production will depend on the rational design and manipulation of industrial strains to improve their robustness against the many stress factors affecting their performance during very high gravity (VHG) or lignocellulosic fermentations. In this study, a set of <it>Saccharomyces cerevisiae </it>genes found, through genome-wide screenings, to confer resistance to the simultaneous presence of different relevant stresses were identified as required for maximal fermentation performance under industrial conditions.</p> <p>Results</p> <p>Chemogenomics data were used to identify eight genes whose expression confers simultaneous resistance to high concentrations of glucose, acetic acid and ethanol, chemical stresses relevant for VHG fermentations; and eleven genes conferring simultaneous resistance to stresses relevant during lignocellulosic fermentations. These eleven genes were identified based on two different sets: one with five genes granting simultaneous resistance to ethanol, acetic acid and furfural, and the other with six genes providing simultaneous resistance to ethanol, acetic acid and vanillin. The expression of <it>Bud31 </it>and <it>Hpr1 </it>was found to lead to the increase of both ethanol yield and fermentation rate, while <it>Pho85</it>, <it>Vrp1 </it>and <it>Ygl024w </it>expression is required for maximal ethanol production in VHG fermentations. Five genes, <it>Erg2</it>, <it>Prs3</it>, <it>Rav1</it>, <it>Rpb4 </it>and <it>Vma8</it>, were found to contribute to the maintenance of cell viability in wheat straw hydrolysate and/or the maximal fermentation rate of this substrate.</p> <p>Conclusions</p> <p>The identified genes stand as preferential targets for genetic engineering manipulation in order to generate more robust industrial strains, able to cope with the most significant fermentation stresses and, thus, to increase ethanol production rate and final ethanol titers.</p

Assessment of circular economy within portuguese organizations

The move towards a new Circular Economy (CE) economic model has been advocated and supported in Portugal, however, there is limited research on this topic. To address this gap, a quantitative research based on an online survey was carried out among 99 Portuguese organizations, encompassing a wide range of sectors and sizes. The results show that CE is regarded as a strategic and relevant issue for profitability and value creation. Furthermore, the perception that it requires the adoption of new business models in addition to the classical “reduce, reuse and recycle” approach is growing. Moreover, based on the hypotheses raised, results suggest that the level of CE adoption is positively impacted by the status of the EMS (Environmental Management System) certification and the willingness to improve the environmental performance and achieve a sustainable business model. However, CE activities are still relatively modest and a friendlier context (fiscal, legal, organizational, etc.) and the stronger support from supply chain agents and consumers are required. Future research should focus on how to design and shape the transition from a linear to a CE economy and to ascertain if the positive attitude towards CE is materialized in changing the way business is done.Authors would like to thank all the respondents’ organizations for their participation and the support from CIDEM, R&D unit. 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/0615/2016. Pedro Domingues benefited from financial support through the FCT post-doc research grantNo. SFRH/BPD/103322/2014. This research is framed with in the scope of Project “PME Sustentável– Projeto nº16129” funded by Portugal 2020 and FEDER.info:eu-repo/semantics/publishedVersio

On the Seismic Vulnerability Assessment of Urban Areas Using Census Data: The Lisbon Metropolitan Area as a Pilot Study Area

This paper presents a procedure for the application of an index-based vulnerability assessment method to the seismic risk assessment of 292,978 reinforced concrete and 152,916 unreinforced masonry buildings in the Lisbon Metropolitan Area (LMA). A singular innovation of this proposed methodology is that it is tailored to be fed with data from the 2011 national population and housing Census. The vulnerability results are then combined with the seismic hazard component into a GIS tool used to map seismic risk across the LMA. The spatial representation of these results highlights the areas of different levels of vulnerability and risk.info:eu-repo/semantics/publishedVersio

Exposure and physical vulnerability indicators to assess seismic risk in urban areas: A step towards a multi-hazard risk analysis

Understanding the impacts of multi-hazard risk in urban areas is a fundamental step towards the adoption of resilience-enhancement and disaster prevention strategies, underpinning institutional adjustments aimed at improving the capacity of the authorities and stakeholders to manage risk. Within this framework, the work presented in this paper seeks to identify and analyze a set of exposure and buildings’ physical vulnerability indicators to be used as input to a parametric-based seismic vulnerability assessment methodology for the unreinforced masonry (URM) building stock of Lisbon Metropolitan Area (LMA). For this approach, data from the 2011 Census survey are used to define the parameters describing the building’s physical vulnerability and characterise the level of exposure in the study area. These results are then combined with the hazard component into a GIS tool. Seismic vulnerability results are presented for the URM building stock in LMA, and a more detailed analysis is conducted for the building stock of Setúbal municipality. Finally, risk outputs are presented and briefly discussed. Ultimately, understanding the impact and extent of multi-hazards can help prioritize resilience-increasing actions and disaster prevention measures to mitigate and manage natural hazards

On the seismic vulnerability assessment of urban areas using census data: The Lisbon metropolitan area as a pilot study area

This paper presents a procedure for the application of an index-based vulnerability assessment method to the seismic risk assessment of 292,978 reinforced concrete and 152,916 unreinforced masonry buildings in the Lisbon Metropolitan Area (LMA). A singular innovation of this proposed methodology is that it is tailored to be fed with data from the 2011 national population and housing Census. The vulnerability results are then combined with the seismic hazard component into a GIS tool used to map seismic risk across the LMA. The spatial representation of these results highlights the areas of different levels of vulnerability and risk

Prototype of an affordable pressure-controlled emergency mechanical ventilator for COVID-19

We present a viable prototype of a simple mechanical ventilator intended as a last resort to ventilate COVID-19 patients. The prototype implements the pressure-controlled continuous mandatory ventilation mode (PC-CMV) with settable breathing rates, inspiration/expiration time ratios and FiO2 modulation. Although safe, the design aims to minimize the use of technical components and those used are common in industry, so its construction may be possible in times of logistical shortage or disruption or in areas with reduced access to technical materials and at a moderate cost, affordable to lower income countries. Most of the device can be manufactured by modest technical means and construction plans are provided.Comment: This version differs from version 2 in that it includes toxicological and bio-safety tests and updated electronic