Biology-guided algorithms:Improved cardiovascular risk prediction and biomarker discovery

Medical research has seen a stark increase in the amount of available data. The sheer volume and complexity of measured variables challenge the use of traditional statistical methods and are beyond the ability of any human to comprehend. Solving this problem demands powerful models capable of capturing the variable interactions and how those are non-linearly related to the condition under study. In this thesis, we first use Machine Learning (ML) methods to achieve better cardiovascular risk prediction/disease biomarker identification and then describe novel bio-inspired algorithms to solve some of the challenges. On the clinical side, we demonstrate how combining targeted plasma proteomics with ML models outperforms traditional clinical risk factors in predicting first-time acute myocardial infarction as well as recurrent atherosclerotic cardiovascular disease. We then shed some light on the pathophysiological pathways involved in heart failure development using a multi-domain ML model. To improve prediction, we develop a novel graph kernel that incorporates protein-protein interaction information, and suggest a manifold mixing algorithm to increase inter-domain information flow in multi-domain models. Finally, we address global model interpretability to uncover the most important variables governing the prediction. Permutation importance is an intuitive and scalable method commonly used in practice, but it is biased in the presence of covariates. We propose a novel framework to disentangle the shared information between covariates, making permutation importance competitive against methodologies where all marginal contributions of a feature are considered, such as SHAP

The γ'-V2O5 Polymorph as an Attractive 2D Cathodic Material for Lithium and Sodium-Ion Batteries

Lithium-ion batteries (LIBs) have been the subject of intense research due to their high energy density and good cycling performance. However, considering the low natural occurrence of Li in the upper continental crust (≈ 35 ppm), great concerns have been expressed over whether the available lithium reserves in the earth will be sufficient to meet the ever-growing requirements for LIB

Testing the Newton second law in the regime of small accelerations

It has been pointed out that the Newtonian second law can be tested in the very small acceleration regime by using the combined movement of the Earth and Sun around the Galactic center of mass. It has been shown that there are only two brief intervals during the year in which the experiment can be completed, which correspond to only two specific spots on the Earth surface. An alternative experimental setup is presented to allow the measurement to be made on Earth at any location and at any time.It has been pointed out that the Newtonian second law can be tested in the very small acceleration regime by using the combined movement of the Earth and Sun around the Galactic center of mass. It has been shown that there are only two brief intervals during the year in which the experiment can be completed, which correspond to only two specific spots on the Earth surface. An alternative experimental setup is presented to allow the measurement to be made on Earth at any location and at any time

Diversity of seed mineral composition of Phaseolus vulgaris L. germplasm

A collection of 155 accessions of ancient Portuguese common beans (Phaseolus vulgaris L.) was evaluated in relation to the content of 8minerals (Zn, Cu, Fe, Mn, Ca, Mg, P and K) important for human nutrition. A high degree of variability for P, Fe, Zn, Cu, Mn and Ca was observed in the collection. Total correlation matrix analysis revealed the existence of two important sets of strong positive correlations (P 0.0001), one involving P, Fe, Zn, Cu and protein, and the other Ca and Mn. The principal component analysis showed that Zn, Fe and Cu are highly correlated to the first component (27% of variability) and Mn and Ca to the second component (22% of the variability). The high mineral variability observed in the seeds of this common bean collection could be useful for the selection of cultivars with higher nutrition value and for the improvement of seed nutrition quality traits

Analytical expressions for the luminescence of dilute quaternary InAs(N,Sb) semiconductors

In this paper, we calculate the luminescence of the dilute quaternary InAs(N,Sb). The incorporation of N leads to a reduction of the energy gap of the host InAs and Sb acts as a surfactant, improves the N incorporation and further reduces the bandgap. This is thus extremely relevant for devices operating in the mid-infrared (MIR) spectral range from 3 to 5 μm. In order to describe this system, the theory starts with the band anticrossing model applied to both conduction and the valence band to generate inputs for analytical approximations that lead to luminescence spectra, including plasma screening, bandgap renormalization and excitonic enhancements. Direct application of the equations leads to good agreement with some recent experimental data

Influence of landscape features and management practices in olive groves for optimized pest control

Trabalho apresentado em XI European Congress Of Entomology, 2-6 July 2018, Nápoles, Itália.N/

Theory and measurements of harmonic generation in semiconductor superlattices with applications in the 100 GHz to 1 THz range

This manuscript describes harmonic generation in semiconductor superlattices, starting from a Nonequilibrium Green's functions input to relaxation rate-type analytical approximations for the Boltzmann Equation in which imperfections in the structure lead to asymmetric current flow and scattering processes under forward and reverse bias. The resulting current-voltage curves and the predicted consequences on harmonic generation, notably the development of even harmonics are in good agreement with experiments. Significant output for frequencies close to 1 THz (7th harmonic) at room temperature, after excitation by a 141 GHz input signal, demonstrate the potential of superlattice devices for GHz-THz applications

Occupational exposure of firefighters to polycyclic aromatic hydrocarbons in non-fire work environments

This work aims to characterize personal exposure of firefighters to polycyclic aromatic hydrocarbons (PAHs) in non-fire work environments (fire stations), and assesses the respective risks. Eighteen PAHs (16 considered by USEPA as priority pollutants, dibenzo[a,l] pyrene and benzo[j] fluoranthene) were monitored in breathing zones of workers at five Portuguese fire stations during a normal shift. The obtained levels of PAHs fulfilled all existent occupational exposure limits as well as air quality guidelines with total concentrations (Sigma PAHs) in range of 46.8-155 ng m(-3). Light compounds (2-3 rings) were the most predominant congeners (74-96% of Sigma PAHs) whereas PAHs with 5-6 rings accounted 3-9% of Sigma PAHs. Fuel and biomass combustions, vehicular traffic emissions, and use of lubricant oils were identified as the main sources of PAHs exposure at the studied fire corporations. Incremental lifetime cancer risks were below the recommend USEPA guideline of 10(-6) and thus negligible for all the studied subjects, but WHO health-based guideline level of 10(-5) was exceeded (9-44 times) at all fire corporations. These results thus show that even during non-fire situations firefighters are exposed to PAHs at levels that may promote some adverse health outcomes; therefore the respective occupational exposures to these compounds should be carefully controlled. (C) 2017This work was supported by European Union (FEDER funds through COMPETE) and National Funds (Fundação para a Ciência e Tecnologia) through projects UID/QUI/50006/2013, POCI/01/0145/FEDER/007265 and UID/EQU/00511/2013-LEPABE, by the FCT/MECwith national funds and co-funded by FEDER in the scope of the P2020 Partnership Agreement. Additional financial support was provided by Fundação para Ciência e Tecnologia through fellowships SFRH/BD/80113/2011 and SFRH/BPD/105100/2014. The authors are thankful to all firefighters involved in the study and to collaborators from Escola Superior de Saúde from Instituto Politécnico de Bragança.info:eu-repo/semantics/publishedVersio

A Singular Conformal Spacetime

The infinite cosmological "constant" limit of the de Sitter solutions to Einstein's equation is studied. The corresponding spacetime is a singular, four-dimensional cone-space, transitive under proper conformal transformations, which constitutes a new example of maximally-symmetric spacetime. Grounded on its geometric and thermodynamic properties, some speculations are made in connection with the primordial universe.Comment: RevTeX4, 10 pages, 1 eps figure. Presentation changes, including a new title; section II.E, on the thermodynamic properties of the de Sitter horizon, completely revised. Version to be published in Journal of Geometry and Physic