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Publications

Publications by BIO

2022

Fast Estimation of the Spectral Optical Properties of Rabbit Pancreas and Pigment Content Analysis

Authors
Martins, IS; Silva, HF; Tuchin, VV; Oliveira, LM;

Publication
PHOTONICS

Abstract
The pancreas is a highly important organ, since it produces insulin and prevents the occurrence of diabetes. Although rare, pancreatic cancer is highly lethal, with a small life expectancy after being diagnosed. The pancreas is one of the organs less studied in the field of biophotonics. With the objective of acquiring information that can be used in the development of future applications to diagnose and treat pancreas diseases, the spectral optical properties of the rabbit pancreas were evaluated in a broad-spectral range, between 200 and 1000 nm. The method used to obtain such optical properties is simple, based almost on direct calculations from spectral measurements. The optical properties obtained show similar wavelength dependencies to the ones obtained for other tissues, but a further analysis on the spectral absorption coefficient showed that the pancreas tissues contain pigments, namely melanin, and lipofuscin. Using a simple calculation, it was possible to retrieve similar contents of these pigments from the absorption spectrum of the pancreas, which indicates that they accumulate in the same proportion as a result of the aging process. Such pigment accumulation was camouflaging the real contents of DNA, hemoglobin, and water, which were precisely evaluated after subtracting the pigment absorption.

2022

Life course of retrospective harmonization initiatives: key elements to consider

Authors
Fortier, I; Wey, TW; Bergeron, J; de Moira, AP; Nybo Andersen, AM; Bishop, T; Murtagh, MJ; Miocevic, M; Swertz, MA; van Enckevort, E; Marcon, Y; Mayrhofer, MT; Ornelas, JP; Sebert, S; Santos, AC; Rocha, A; Wilson, RC; Griffith, LE; Burton, P;

Publication
JOURNAL OF DEVELOPMENTAL ORIGINS OF HEALTH AND DISEASE

Abstract
Optimizing research on the developmental origins of health and disease (DOHaD) involves implementing initiatives maximizing the use of the available cohort study data; achieving sufficient statistical power to support subgroup analysis; and using participant data presenting adequate follow-up and exposure heterogeneity. It also involves being able to undertake comparison, cross-validation, or replication across data sets. To answer these requirements, cohort study data need to be findable, accessible, interoperable, and reusable (FAIR), and more particularly, it often needs to be harmonized. Harmonization is required to achieve or improve comparability of the putatively equivalent measures collected by different studies on different individuals. Although the characteristics of the research initiatives generating and using harmonized data vary extensively, all are confronted by similar issues. Having to collate, understand, process, host, and co-analyze data from individual cohort studies is particularly challenging. The scientific success and timely management of projects can be facilitated by an ensemble of factors. The current document provides an overview of the 'life course' of research projects requiring harmonization of existing data and highlights key elements to be considered from the inception to the end of the project.

2022

Estimation of ANT-DBS Electrodes on Target Positioning Based on a New Percept (TM) PC LFP Signal Analysis

Authors
Lopes, EM; Rego, R; Rito, M; Chamadoira, C; Dias, D; Cunha, JPS;

Publication
SENSORS

Abstract
Deep brain stimulation of the Anterior Nucleus of the Thalamus (ANT-DBS) is an effective therapy in epilepsy. Poorer surgical outcomes are related to deviations of the lead from the ANT-target. The target identification relies on the visualization of anatomical structures by medical imaging, which presents some disadvantages. This study aims to research whether ANT-LFPs recorded with the Percept (TM) PC neurostimulator can be an asset in the identification of the DBS-target. For this purpose, 17 features were extracted from LFPs recorded from a single patient, who stayed at an Epilepsy Monitoring Unit for a 5-day period. Features were then integrated into two machine learning (ML)-based methodologies, according to different LFP bipolar montages: Pass1 (nonadjacent channels) and Pass2 (adjacent channels). We obtained an accuracy of 76.6% for the Pass1-classifier and 83.33% for the Pass2-classifier in distinguishing locations completely inserted in the target and completely outside. Then, both classifiers were used to predict the target percentage of all combinations, and we found that contacts 3 (left hemisphere) and 2 and 3 (right hemisphere) presented higher signatures of the ANT-target, which agreed with the medical images. This result opens a new window of opportunity for the use of LFPs in the guidance of DBS target identification.

2022

Towards real-time identification of trapped particles with UMAP-based classifiers

Authors
Teixeira, J; Rocha, V; Oliveira, J; Jorge, PAS; Silva, NA;

Publication
Journal of Physics: Conference Series

Abstract
Optical trapping provides a way to isolate, manipulate, and probe a wide range of microscopic particles. Moreover, as particle dynamics are strongly affected by their shape and composition, optical tweezers can also be used to identify and classify particles, paving the way for multiple applications such as intelligent microfluidic devices for personalized medicine purposes, or integrated sensing for bioengineering. In this work, we explore the possibility of using properties of the forward scattered radiation of the optical trapping beam to analyze properties of the trapped specimen and deploy an autonomous classification algorithm. For this purpose, we process the signal in the Fourier domain and apply a dimensionality reduction technique using UMAP algorithms, before using the reduced number of features to feed standard machine learning algorithms such as K-nearest neighbors or random forests. Using a stratified 5-fold cross-validation procedure, our results show that the implemented classification strategy allows the identification of particle material with accuracies up to 80%, demonstrating the potential of using signal processing techniques to probe properties of optical trapped particles based on the forward scattered light. Furthermore, preliminary results of an autonomous implementation in a standard experimental optical tweezers setup show similar differentiation capabilities for real-time applications, thus opening some opportunities towards technological applications such as intelligent microfluidic devices and solutions for biochemical and biophysical sensing. © Published under licence by IOP Publishing Ltd.

2022

Autonomous Optical Tweezers: From automatic trapping to single particle analysis

Authors
Coutinho, F; Teixeira, J; Rocha, V; Oliveira, J; Jorge, PAS; Silva, NA;

Publication
Journal of Physics: Conference Series

Abstract
Optical trapping is a versatile and non-invasive technique for single particle manipulation. As such, it can be widely applied in the domains of particle identification and classification and thus used as a tool for monitoring physical and chemical processes. This creates an opportunity for integrating the method seamlessly into optofluidic chips, provided it can be automatized. Yet even though OT is well established in multiple scientific domains, a full stack approach to its integration into other technological devices is still lacking. This calls for solutions in tasks such as automatic trapping and signal analysis. In this manuscript, we describe the implementation of an algorithm seeking autonomous particle location and trapping. The methodology is based upon image-processing, allowing for particle location using real time image segmentation. A local thresholding algorithm is applied, followed by morphological techniques for closing shapes and excluding non-bounded regions - after which only the particles remain on the image. Once the centroid is identified, the stage is translated accordingly by piezo-electric actuators, followed by the laser activation. In this way, trapping is achieved, and one may proceed to analyze the forward scattered optical signal, after which a new particle inside the actuators range may be automatically trapped. This development, when compared with existent solutions involving holographic optical tweezers, allows for similar capabilities without using a spatial light modulator, thus dramatically reducing the setup costs of autonomous OT solutions. Therefore, when combined with particle classification techniques, this method is well suited for integration into possible optofluidic chips for autonomous sensing and monitoring of biochemical samples. © Published under licence by IOP Publishing Ltd.

2022

Unscrambling spectral interference and matrix effects in Vitis vinifera Vis-NIR spectroscopy: Towards analytical grade 'in vivo' sugars and acids quantification

Authors
Martins, RC; Barroso, TG; Jorge, P; Cunha, M; Santos, F;

Publication
COMPUTERS AND ELECTRONICS IN AGRICULTURE

Abstract
Analytical grade 'in vivo' plant metabolic quantification using spectroscopy is a key enabling technology for precision agriculture.Current methods such as PLS, ANN and LS-SVM are non-optimal for resolving spectral interference and matrix effects to provide similar results to the analytical chemistry laboratory. This research presents a new self-learning artificial intelligence (SL-AI) method based on the search of covariance modes. These isolate the different modes of interference present in spectral data, allowing the consistent quantification of constituents. A review of the state-of-the-art methods with the figures of merit mean absolute standard error percentage (MASEP) and Pearson correlation coefficient (R) is presented for comparison and discussion. 707 grapes were quantified for glucose, fructose, malic and tartaric acids in five wine-making and one table grape varieties, and used to benchmark the new method against the state-of-the-art methodologies: partial least squares, local partial least squares, artificial neural networks and least squares support vector machines. SL-AI provides consistent quantifications, whereas previous methods exhibit data-driven performance dependence. Pearson correlations of 0.93 to 0.99 and MASEP of 3.70% to 7.33% were obtained with the new methodology. Local partial least squares, the method with the best benchmarks from literature, achieved correlations of 0.81 to 0.94 and MASEP of 8.00% to 13.4%. The covariance mode isolates a particular interference, providing a direct relationship between spectral inference and constituent concentrations, consistent with the Beer-Lambert law. Such quantifies non-dominant absorbance constituents (e.g. sugars and acids), which is a significant step towards 'in vivo' plant physiology-based precision agriculture.

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