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Publications

2025

Comparing 2D and 3D Feature Extraction Methods for Lung Adenocarcinoma Prediction Using CT Scans: A Cross-Cohort Study

Authors
Gouveia, M; Mendes, T; Rodrigues, EM; Oliveira, HP; Pereira, T;

Publication
APPLIED SCIENCES-BASEL

Abstract
Lung cancer stands as the most prevalent and deadliest type of cancer, with adenocarcinoma being the most common subtype. Computed Tomography (CT) is widely used for detecting tumours and their phenotype characteristics, for an early and accurate diagnosis that impacts patient outcomes. Machine learning algorithms have already shown the potential to recognize patterns in CT scans to classify the cancer subtype. In this work, two distinct pipelines were employed to perform binary classification between adenocarcinoma and non-adenocarcinoma. Firstly, radiomic features were classified by Random Forest and eXtreme Gradient Boosting classifiers. Next, a deep learning approach, based on a Residual Neural Network and a Transformer-based architecture, was utilised. Both 2D and 3D CT data were initially explored, with the Lung-PET-CT-Dx dataset being employed for training and the NSCLC-Radiomics and NSCLC-Radiogenomics datasets used for external evaluation. Overall, the 3D models outperformed the 2D ones, with the best result being achieved by the Hybrid Vision Transformer, with an AUC of 0.869 and a balanced accuracy of 0.816 on the internal test set. However, a lack of generalization capability was observed across all models, with the performances decreasing on the external test sets, a limitation that should be studied and addressed in future work.

2025

Tartrazine for Optical Clearing of Tissues: Stability and Diffusion Issues

Authors
Guerra, AR; Oliveira, LR; Rodrigues, GO; Pinheiro, MR; Carvalho, MI; Tuchin, VV; Oliveira, LM;

Publication
JOURNAL OF BIOPHOTONICS

Abstract
Measuring the density of tartrazine (TZ) powder allowed to develop a protocol for fast preparation of aqueous solutions with a desired concentration. The stability time of these solutions decreases exponentially with the increase of TZ concentration: solutions with TZ concentrations below 25% remain stable for more than 24 h, while the solution with 60% TZ remains stable only for 35 min. To validate the developed protocol, muscle samples were immersed in the 40% TZ solution and, as expected, the tissue transparency increased smoothly and exponentially during the whole treatment of 30 min. The diffusion time of TZ in ex vivo skeletal muscle was quantitatively determined with high accuracy as tau TZ = 5.39 +/- 0.49 min for sample thickness of 0.5 mm. By measuring the refractive index of TZ solutions during preparation, it will be easier to prepare such solutions in a fast manner for future research on tissue optical clearing.

2025

Do We Need 3D to See? Impact of Dimensionality of the Virtual Environment on Attention

Authors
Matos, T; Mendes, D; Jacob, J; de Sousa, AA; Rodrigues, R;

Publication
IEEE Conference on Virtual Reality and 3D User Interfaces, VR 2025 - Abstracts and Workshops, Saint Malo, France, March 8-12, 2025

Abstract
Virtual Reality allows users to experience realistic environments in an immersive and controlled manner, particularly beneficial for contexts where the real scenario is not easily or safely accessible. The choice between 360° content and 3D models impacts outcomes such as perceived quality and computational cost, but can also affect user attention. This study explores how attention manifests in VR using a 3D model or a 360° image rendered from said model during visuospatial tasks. User tests revealed no significant difference in workload or cybersickness between these types of content, while sense of presence was reportedly higher in the 3D environment. © 2025 IEEE.

2025

Quartic soliton solutions of a normal-dispersion-based mode-locked laser

Authors
Facao, M; Malheiro, D; Carvalho, MI;

Publication
PHYSICAL REVIEW A

Abstract
We studied the characteristics, regions of existence, and stability of different types of solitons for a distributed model of a mode-locked laser whose dispersion is purely quartic and normal. Among the different types of solitons, we identified three main branches that are named according to their different amplitude: low, medium, and high amplitude solitons. It was found that the first solitons are always unstable while the latter two exist and are stable in relatively large regions of the parameter space. Moreover, the stability regions of medium and high amplitude solitons overlap over a certain range of parameters, manifesting effects of bistability. The energy of high amplitude solitons increases quadratically with their width, whereas the energy of medium amplitude solitons may decrease or increase with the width depending on the parameter region. Furthermore, we have investigated the long term evolution of the continuous-wave solutions under modulational instability, showing that medium amplitude solitons can arise in this scenario. Additionally, we assessed the effects of second- and third-order dispersion on medium and high amplitude solitons and found that both remain stable in the presence of these terms.

2024

Community detection in interval-weighted networks

Authors
Alves, H; Brito, P; Campos, P;

Publication
DATA MINING AND KNOWLEDGE DISCOVERY

Abstract
In this paper we introduce and develop the concept of interval-weighted networks (IWN), a novel approach in Social Network Analysis, where the edge weights are represented by closed intervals composed with precise information, comprehending intrinsic variability. We extend IWN for both Newman's modularity and modularity gain and the Louvain algorithm, considering a tabular representation of networks by contingency tables. We apply our methodology to two real-world IWN. The first is a commuter network in mainland Portugal, between the twenty three NUTS 3 Regions (IWCN). The second focuses on annual merchandise trade between 28 European countries, from 2003 to 2015 (IWTN). The optimal partition of geographic locations (regions or countries) is developed and compared using two new different approaches, designated as Classic Louvain and Hybrid Louvain , which allow taking into account the variability observed in the original network, thereby minimizing the loss of information present in the raw data. Our findings suggest the division of the twenty three Portuguese regions in three main communities for the IWCN and between two to three country communities for the IWTN. However, we find different geographical partitions according to the community detection methodology used. This analysis can be useful in many real-world applications, since it takes into account that the weights may vary within the ranges, rather than being constant.

2024

A field-based evaluation of portable XRF to screen for toxic metals in seafood products

Authors
Roberts, AA; Guimaraes, D; Tehrani, MW; Lin, S; Parsons, PJ;

Publication
X-RAY SPECTROMETRY

Abstract
Portable X-Ray Fluorescence (XRF) has become increasingly popular where traditional laboratory methods are either impractical, time consuming, and/or too costly. While the Limit of Detection (LOD) is generally poorer for XRF compared to laboratory-based methods, recent advances have improved XRF LODs and increased its potential for field-based studies. Portable XRF can be used to screen food products for toxic elements such as lead (Pb), cadmium (Cd), mercury (Hg), arsenic (As), manganese, (Mn), zinc (Zn), and strontium (Sr). In this study, 23 seafood samples were analyzed using portable XRF in a home setting. After XRF measurements were completed in each home, the same samples were transferred to the laboratory for re-analysis using microwave-assisted digestion and Inductively Coupled Plasma Tandem Mass Spectrometry (ICP-MS/MS). Four elements (Mn, Sr, As, and Zn) were quantifiable by XRF in most samples, and those results were compared to those obtained by ICP-MS/MS. Agreement was judged reasonable for Mn, Sr, and As, but not for Zn. Discrepancies could be due to (1) the limited time available to prepare field samples for XRF, (2) the heterogeneous nature of real samples analyzed by XRF, and (3) the small beam spot size (similar to 1 mm) of the XRF analyzer. Portable XRF is a cost-effective screening tool for public health investigations involving exposure to toxic metals. It is important for practitioners untrained in XRF spectrometry to (1) recognize the limitations of portable instrumentation, (2) include validation data for each specific analyte(s) measured, and (3) ensure personnel have some training in sample preparation techniques for field-based XRF analyses.

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