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Publications

Publications by BIO

2023

Transmissive glucose concentration plasmonic Au sensor based on unclad optical fiber

Authors
Cunha, C; Assuncao, AS; Monteiro, CS; Leitao, C; Mendes, JP; Silva, S; Frazao, O; Novais, S;

Publication
2023 IEEE 7TH PORTUGUESE MEETING ON BIOENGINEERING, ENBENG

Abstract
Using surface resonance (SPR) as a sensitivity enhancer, this work describes the development of a transmissive multimode optical fiber sensor with a gold (Au) thin film that measures glucose concentration. The fiber's cladding was initially removed, and an Au layer was then sputtered onto its surface to simultaneously excite SPR and reflect light, making the SPR sensor extremely sensitive to changes in the environment's refractive index. A range of glucose concentrations, from 0.0001 to 0.5000 g/ml, were tested on the sensor. A maximum sensitivity of 161.302 nm/(g/mL) was attained for the lowest glucose concentration, while the highest concentration yielded a sensitivity of 312.000 nm/(g/mL). The proposed sensor's compact size, high sensitivity, good stability and practicality make it a promising candidate for a range of applications, including detecting diabetes.

2023

Paracetamol concentration-sensing scheme based on a linear cavity fiber laser configuration

Authors
Soares, L; Perez Herrera, RA; Novais, S; Ferreira, A; Fraza, O; Silva, S;

Publication
OPTICAL FIBER TECHNOLOGY

Abstract
A paracetamol concentration-sensing scheme based on a linear cavity fiber laser configuration is demonstrated experimentally. The laser cavity has a fiber sensor at one end, that allows refractive index measurements. The refractometer consists of a cleaved fiber tip combined with an FBG functioning as a reflecting mirror. The combination of a fiber loop mirror at the other end allows to reflect all the light from the FBG and refractometer, forming a linear cavity. By measuring the intensity variation of the Fresnel reflection at the fiber-to-liquid interface, the measured concentration is linear and have a concentration sensitivity of [( - 8.74 & PLUSMN; 0.34) x 10-5 ] & mu;W/(g/kg), over a range of 52.61 to 219.25 g/kg, and with a resolution of 2.77 g/kg. The results obtained present high stability and prove the potential of the fiber laser system to performed realtime measurements of concentration, in a non-invasive way.

2023

Automatic Eye-Tracking-Assisted Chest Radiography Pathology Screening

Authors
Santos, R; Pedrosa, J; Mendonça, AM; Campilho, A;

Publication
Pattern Recognition and Image Analysis - 11th Iberian Conference, IbPRIA 2023, Alicante, Spain, June 27-30, 2023, Proceedings

Abstract

2023

A systematic evaluation of deep learning methods for the prediction of drug synergy in cancer

Authors
Baptista, D; Ferreira, PG; Rocha, M;

Publication
PLOS COMPUTATIONAL BIOLOGY

Abstract
Author summaryCancer therapies often fail because tumor cells become resistant to treatment. One way to overcome resistance is by treating patients with a combination of two or more drugs. Some combinations may be more effective than when considering individual drug effects, a phenomenon called drug synergy. Computational drug synergy prediction methods can help to identify new, clinically relevant drug combinations. In this study, we developed several deep learning models for drug synergy prediction. We examined the effect of using different types of deep learning architectures, and different ways of representing drugs and cancer cell lines. We explored the use of biological prior knowledge to select relevant cell line features, and also tested data-driven feature reduction methods. We tested both precomputed drug features and deep learning methods that can directly learn features from raw representations of molecules. We also evaluated whether including genomic features, in addition to gene expression data, improves the predictive performance of the models. Through these experiments, we were able to identify strategies that will help guide the development of new deep learning models for drug synergy prediction in the future. One of the main obstacles to the successful treatment of cancer is the phenomenon of drug resistance. A common strategy to overcome resistance is the use of combination therapies. However, the space of possibilities is huge and efficient search strategies are required. Machine Learning (ML) can be a useful tool for the discovery of novel, clinically relevant anti-cancer drug combinations. In particular, deep learning (DL) has become a popular choice for modeling drug combination effects. Here, we set out to examine the impact of different methodological choices on the performance of multimodal DL-based drug synergy prediction methods, including the use of different input data types, preprocessing steps and model architectures. Focusing on the NCI ALMANAC dataset, we found that feature selection based on prior biological knowledge has a positive impact-limiting gene expression data to cancer or drug response-specific genes improved performance. Drug features appeared to be more predictive of drug response, with a 41% increase in coefficient of determination (R-2) and 26% increase in Spearman correlation relative to a baseline model that used only cell line and drug identifiers. Molecular fingerprint-based drug representations performed slightly better than learned representations-ECFP4 fingerprints increased R-2 by 5.3% and Spearman correlation by 2.8% w.r.t the best learned representations. In general, fully connected feature-encoding subnetworks outperformed other architectures. DL outperformed other ML methods by more than 35% (R-2) and 14% (Spearman). Additionally, an ensemble combining the top DL and ML models improved performance by about 6.5% (R-2) and 4% (Spearman). Using a state-of-the-art interpretability method, we showed that DL models can learn to associate drug and cell line features with drug response in a biologically meaningful way. The strategies explored in this study will help to improve the development of computational methods for the rational design of effective drug combinations for cancer therapy.

2023

Invasive and Minimally Invasive Evaluation of Diffusion Properties of Sugar in Muscle

Authors
Pinheiro, MR; Tuchin, VV; Oliveira, LM;

Publication
IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS

Abstract
In this article, the use of diffuse reflectance (R-d) spectroscopy is explored to evaluate the diffusion properties of water and sucrose in skeletal muscle during optical clearing treatments. Treating muscle samples with sucrose-water solutions with different osmolarities, collimated transmittance (T-c) and R-d measurements were performed to obtain the diffusion time (t) and the diffusion coefficient (D) values that characterize the unique water and sucrose fluxes in the muscle and also the optical clearing mechanisms designated as tissue dehydration and refractive index matching. Considering the R-d measurements, the estimated t and D values for water in the muscle were 63.1s and 1.72x10(-6) cm(2)/s, while the ones estimated for sucrose were 261s and 4.86x10(-7) cm(2)/s. Comparing these values with the ones estimated from the T-c measurements, the relative differences observed for t and D were 1.6% and 2.8% in the case of water and 0.3% and 0.4% in the case of sucrose.

2023

Measurement of tissue optical properties in a wide spectral range: a review [Invited]

Authors
Martins, IS; Silva, HF; Lazareva, EN; Chernomyrdin, NV; Zaytsev, KI; Oliveira, LM; Tuchin, VV;

Publication
BIOMEDICAL OPTICS EXPRESS

Abstract
A distinctive feature of this review is a critical analysis of methods and results of measurements of the optical properties of tissues in a wide spectral range from deep UV to terahertz waves. Much attention is paid to measurements of the refractive index of biological tissues and liquids, the knowledge of which is necessary for the effective application of many methods of optical imaging and diagnostics. The optical parameters of healthy and pathological tissues are presented, and the reasons for their differences are discussed, which is important for the discrimination of pathologies and the demarcation of their boundaries. When considering the interaction of terahertz radiation with tissues, the concept of an effective medium is discussed, and relaxation models of the effective optical properties of tissues are presented. Attention is drawn to the manifestation of the scattering properties of tissues in the THz range and the problems of measuring the optical properties of tissues in this range are discussed. In conclusion, a method for the dynamic analysis of the optical properties of tissues under optical clearing using an application of immersion agents is presented. The main mechanisms and technologies of optical clearing, as well as examples of the successful application for differentiation of healthy and pathological tissues, are analyzed. (c) 2022 Optica Publishing Group under the terms of the Optica Open Access Publishing Agreement

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