8,045 research outputs found
Reproducible research using biomodels
Like other types of computational research, modeling and simulation of
biological processes (biomodels) is still largely communicated without
sufficient detail to allow independent reproduction of results. But
reproducibility in this area of research could easily be achieved by making use
of existing resources, such as supplying models in standard formats and
depositing code, models, and results in public repositories
Reproducibility and FAIR Principles: The Case of a Segment Polarity Network Model
The issue of reproducibility of computational models and the related FAIR
principles (findable, accessible, interoperable, and reusable) are examined in
a specific test case. I analyze a computational model of the segment polarity
network in Drosophila embryos published in 2000. Despite the high number of
citations to this publication, 23 years later the model is barely accessible,
and consequently not interoperable. Following the text of the original
publication allowed successfully encoding the model for the open source
software COPASI. Subsequently saving the model in the SBML format allowed it to
be reused in other open source software packages. Submission of this SBML
encoding of the model to the BioModels database enables its findability and
accessibility. This demonstrates how the FAIR principles can be successfully
enabled by using open source software, widely adopted standards, and public
repositories, facilitating reproducibility and reuse of computational cell
biology models that will outlive the specific software used
what can music tell about the history of a colonial city?
UID/EAT/00472/2019publishersversionpublishe
Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism
To be viable, organisms possess a number of (deoxy)nucleotide phosphohydrolases, which hydrolyze these nucleotides removing them from the active NTP and dNTP pools.
Deamination of purine bases can result in accumulation of
such nucleotides as ITP, dITP, XTP and dXTP. E. coli RdgB has been characterised as a deoxyribonucleoside triphosphate pyrophosphohydrolase that can act on these nucleotides. S. cerevisiae homologue encoded by YJR069C was purified and its (d)NTPase activity was assayed using fifteen nucleotide substrates. ITP, dITP, and XTP were identified as major substrates
and kinetic parameters measured. Inhibition by ATP,
dATP and GTP were established. On the basis of experimental and published data, modelling and simulation of ITP, dITP, XTP and dXTP metabolism was performed. (d)ITP/(d)XTPase is a new example of enzyme with multiple substrate-specificity demonstrating that multispecificity is not a rare phenomenon
Correction of spatial distortion in magnetic resonance imaging
Dissertation to Obtain the Degree of Master
in Biomedical EngineeringMagnetic Resonance Imaging (MRI) has been a major investigation and research focus among
scientific and medical communities. So, new hardware with superior magnetic fields and faster sequences has been developed. However, these improvements result in intensity and spatial distortions, particularly in fast sequences, as Echo Plana Imaging (EPI), used in functional and
diffusion-weighed MRI (fMRI and DW-MRI). Therefore, correction of spatial distortion is useful to obtain a higher quality in this kind of images.
This project contains two major parts. The first part consists in simulating MRI data required for assessing the performance of Registration methods and optimizing parameters. To assess the methods five evaluation metrics were calculated between the corrected data and an undistorted EPI, namely: Root Mean Square (RMS); Normalized Mutual Information (NMI), Squared Correlation
Coefficient(SCC); Euclidean Distance of Centres of Mass (CM) and Dice Coefficient of
segmented images. In brief, this part validates the applied Registration correction method. The project’s second part includes correction of real images, obtained at a Clinical Partner. Real images are diffusion weighted MRI data with different b-values (gradient strength coefficient), allowing performance assessment of different methods on images with increasing b-values and decreasing SNR. The methods tested on real data were Registration, Field Map correction and a new proposed pipeline, which consists in performing a Field Map correction after a registration process.
To assess the accuracy of these methods on real data, we used the same evaluation metrics, as for simulated data, except RMS and Dice Coefficient.
At the end, it was concluded that Registration-based methods are better than Field Map, and that the new proposed pipeline produces some improvements in the registration. Regarding the influence of b-value on the correction, it is important to say that the methods performed using images with higher b’s showed more improvements in regarding metric values, but the behaviour is similar for all b-values
Pathophysiological Role and Therapeutic potential of Neuregulin-1 in Pulmonary Arterial Hypertension
Autonomous Assessment of Videogame Difficulty Using Physiological Signals
Given the well-explored relation between challenge and involvement in a task, (e.g.,
as described in Csikszentmihalyi’s theory of flow), it could be argued that the presence
of challenge in videogames is a core element that shapes player experiences and should,
therefore, be matched to the player’s skills and attitude towards the game. However,
handling videogame difficulty, is a challenging problem in game design, as too easy a
task can lead to boredom and too hard can lead to frustration. Thus, by exploring the
relationship between difficulty and emotion, the current work intends to propose an
artificial intelligence model that autonomously predicts difficulty according to the set
of emotions elicited in the player. To test the validity of this approach, we developed
a simple puzzle-based Virtual Reality (VR) videogame, based on the Trail Making Test
(TMT), and whose objective was to elicit different emotions according to three levels of
difficulty. A study was carried out in which physiological responses as well as player self-
reports were collected during gameplay. Statistical analysis of the self-reports showed
that different levels of experience with either VR or videogames didn’t have a measurable
impact on how players performed during the three levels. Additionally, the self-assessed
emotional ratings indicated that playing the game at different difficulty levels gave rise to
different emotional states. Next, classification using a Support Vector Machine (SVM) was
performed to verify if it was possible to detect difficulty considering the physiological
responses associated with the elicited emotions. Results report an overall F1-score of 68%
in detecting the three levels of difficulty, which verifies the effectiveness of the adopted
methodology and encourages further research with a larger dataset.Dada a relação bem explorada entre desafio e envolvimento numa tarefa (p. ex., con-
forme descrito na teoria do fluxo de Csikszentmihalyi), pode-se argumentar que a pre-
sença de desafio em videojogos é um elemento central que molda a experiência do jogador
e deve, portanto, ser compatÃvel com as habilidades e a atitude que jogador exibe perante
o jogo. No entanto, saber como lidar com a dificuldade de um videojogo é um problema
desafiante no design de jogos, pois uma tarefa muito fácil pode gerar tédio e muito di-
fÃcil pode levar à frustração. Assim, ao explorar a relação entre dificuldade e emoção,
o presente trabalho pretende propor um modelo de inteligência artificial que preveja
de forma autônoma a dificuldade de acordo com o conjunto de emoções elicitadas no
jogador. Para testar a validade desta abordagem, desenvolveu-se um jogo de puzzle em
Realidade Virtual (RV), baseado no Trail Making Test (TMT), e cujo objetivo era elicitar
diferentes emoções tendo em conta três nÃveis de dificuldade. Foi realizado um estudo no
qual se recolheram as respostas fisiológicas, juntamente com os autorrelatos dos jogado-
res, durante o jogo. A análise estatÃstica dos autorelatos mostrou que diferentes nÃveis de
experiência com RV ou videojogos não tiveram um impacto mensurável no desempenho
dos jogadores durante os três nÃveis. Além disso, as respostas emocionais auto-avaliadas
indicaram que jogar o jogo em diferentes nÃveis de dificuldade deu origem a diferentes
estados emocionais. Em seguida, foi realizada a classificação por intermédio de uma Má-
quina de Vetores de Suporte (SVM) para verificar se era possÃvel detectar dificuldade,
considerando as respostas fisiológicas associadas às emoções elicitadas. Os resultados re-
latam um F1-score geral de 68% na detecção dos três nÃveis de dificuldade, o que verifica
a eficácia da metodologia adotada e incentiva novas pesquisas com um conjunto de dados
maior
The impact of electric vehicles on the transportion setor
Due to the continuous useage of fossil fuels we are almost reaching a point of no return with catastrophic consequences in terms of climate change. With this issue in mind some companies, specifically in the automotive industry, have decided to go green with several BEV fleets which are changing and forcing cities to adapt to these changes and to the new APV options appearing with the purpose of enhencing and facilitate the mobility inside the cities. In this sense, the present investigation aims to estimate the impact and changes in the portuguese transportation sector, as well to assess the customer perception and identify the decision-making factors of an electric vehicle. An online questionnaire was used as a mean to collect the higher and broader number of respondents and its analysis was performed based on a qualitative analysis, hypothesis testing and correlations.
The results predict a growth of the APV in Europe and in Portugal along with average age of the Portuguese automotive car parc. It also expected a growth of the charging points infrastructure and the mobility options within the city. A BEV buyer usually considers itself as an ambitious person, seeking for new information about technology, sociable and always looking for ways to improve their life’s and considers the running costs of an EV to be lower than a conventional car. Moreover, the Price and Autonomy are the two most valued factors in an EV and the Brand and Technology the least.Devido ao uso continuado dos combustÃveis fósseis, nós estamos a chegar a um ponto de não retorno com consequências devastadoras em termos de alterações climáticas. Com esta questão em mente, algumas empresas, especificamente da indústria automóvel, decidiram ser mais sustentáveis com o desenvolvimento de vários BEV nas suas frotas que estão a mudar e forçar as cidades a adaptarem-se a estas novas mudanças e ainda, à s novas opções de APV que estão a aparecer com o objetivo de melhorar e facilitar a mobilidade dentro das cidades. Deste modo, a presente investigação serve para estimar o impacto e as mudanças no setor dos transportes em Portugal, bem como entender a perceção do comprador e identificar os fatores decisão num automóvel elétrico. Um questionário online foi efetuado de maneira a conseguir recolher o maior e mais variado número de inquiridos e a sua análise foi feita com base numa análise qualitativa, teste de hipóteses e correlações.
Os resultados preveem um crescimento dos APV na Europa e em Portugal juntamente com o crescimento da idade média do parque automóvel português. Também é esperado um aumento da infraestrutura de pontos de carregamento e das opções de mobilidade dentro da cidade. Uma pessoa que compre um BEV considera se uma pessoa ambiciosa, procurando informação nova sobre tecnologia, sociável, sempre tentando melhorar a sua vida e considera que os custos de manutenção de um automóvel elétrico são inferiores aos de um veÃculo convencional. Além do mais, o Preço e a Autonomia são os dois fatores mais valorizados num EV e a Marca e a Tecnologia os menos valorizados
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