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Publications

Publications by Rui Costa Martins

2022

Kiwi Plant Canker Diagnosis Using Hyperspectral Signal Processing and Machine Learning: Detecting Symptoms Caused by Pseudomonas syringae pv. actinidiae

Authors
Reis Pereira, M; Tosin, R; Martins, R; dos Santos, FN; Tavares, F; Cunha, M;

Publication
PLANTS-BASEL

Abstract
Pseudomonas syringae pv. actinidiae (Psa) has been responsible for numerous epidemics of bacterial canker of kiwi (BCK), resulting in high losses in kiwi production worldwide. Current diagnostic approaches for this disease usually depend on visible signs of the infection (disease symptoms) to be present. Since these symptoms frequently manifest themselves in the middle to late stages of the infection process, the effectiveness of phytosanitary measures can be compromised. Hyperspectral spectroscopy has the potential to be an effective, non-invasive, rapid, cost-effective, high-throughput approach for improving BCK diagnostics. This study aimed to investigate the potential of hyperspectral UV-VIS reflectance for in-situ, non-destructive discrimination of bacterial canker on kiwi leaves. Spectral reflectance (325-1075 nm) of twenty plants were obtained with a handheld spectroradiometer in two commercial kiwi orchards located in Portugal, for 15 weeks, totaling 504 spectral measurements. Several modeling approaches based on continuous hyperspectral data or specific wavelengths, chosen by different feature selection algorithms, were tested to discriminate BCK on leaves. Spectral separability of asymptomatic and symptomatic leaves was observed in all multi-variate and machine learning models, including the FDA, GLM, PLS, and SVM methods. The combination of a stepwise forward variable selection approach using a support vector machine algorithm with a radial kernel and class weights was selected as the final model. Its overall accuracy was 85%, with a 0.70 kappa score and 0.84 F-measure. These results were coherent with leaves classified as asymptomatic or symptomatic by visual inspection. Overall, the findings herein reported support the implementation of spectral point measurements acquired in situ for crop disease diagnosis.

2022

Point-of-Care Using Vis-NIR Spectroscopy for White Blood Cell Count Analysis

Authors
Barroso, TG; Ribeiro, L; Gregorio, H; Monteiro Silva, F; dos Santos, FN; Martins, RC;

Publication
CHEMOSENSORS

Abstract
Total white blood cells count is an important diagnostic parameter in both human and veterinary medicines. State-of-the-art is performed by flow cytometry combined with light scattering or impedance measurements. Spectroscopy point-of-care has the advantages of miniaturization, low sampling, and real-time hemogram analysis. While white blood cells are in low proportions, while red blood cells and bilirubin dominate spectral information, complicating detection in blood. We performed a feasibility study for the direct detection of white blood cells counts in canine blood by visible-near infrared spectroscopy for veterinary applications, benchmarking current chemometrics techniques (similarity, global and local partial least squares, artificial neural networks and least-squares support vector machines) with self-learning artificial intelligence, introducing data augmentation to overcome the hurdle of knowledge representativity. White blood cells count information is present in the recorded spectra, allowing significant discrimination and equivalence between hemogram and spectra principal component scores. Chemometrics methods correlate white blood cells count to spectral features but with lower accuracy. Self-Learning Artificial Intelligence has the highest correlation (0.8478) and a small standard error of 6.92 x 10(9) cells/L, corresponding to a mean absolute percentage error of 25.37%. Such allows the accurate diagnosis of white blood cells in the range of values of the reference interval (5.6 to 17.8 x 10(9) cells/L) and above. This research is an important step toward the existence of a miniaturized spectral point-of-care hemogram analyzer.

2025

Metabolic mapping for precision grape maturation: Application of a tomography-like method for site-specific management

Authors
Tosin, R; Rodrigues, L; Santos-Campos, M; Gonçalves, I; Barbosa, C; Santos, F; Martins, R; Cunha, M;

Publication
SMART AGRICULTURAL TECHNOLOGY

Abstract
This study demonstrates the application of a tomography-like (TL) method to monitor grape maturation dynamics over two growing seasons (2021-2022) in the Douro Wine Region. Using a Vis-NIR point-of-measurement sensor, which employs visible and near-infrared light to penetrate grape tissues non-destructively and provide spectral data to predict internal composition, this approach captures non-destructive measurements of key physicochemical properties, including soluble solids content (SSC), weight-to-volume ratio, chlorophyll and anthocyanin levels across internal grape tissues-skin, pulp, and seeds-over six post-veraison stages. The collected data were used to generate detailed metabolic maps of maturation, integrating topographical factors such as altitude and NDVI-based (normalised difference vegetation index) vigour assessments, which revealed significant (p < 0.05) variations in SSC, chlorophyll, and anthocyanin levels across vineyard zones. The metabolic maps generated from the TL method enable high-throughput data to reveal the impact of environmental variability on grape maturation across distinct vineyard areas. Predictive models using random forest (RF) and self-learning artificial intelligence (SL-AI) algorithms showed RF's robustness, achieving stable predictions with R-2 >= 0.86 and MAPE <= 33.83 %. To illustrate the TL method's practical value, three hypothetical decision models were developed for targeted winemaking objectives based on SSC, chlorophyll in the pulp, and anthocyanin in the skin and seeds. These models underscore the TL method's ability to support site-specific management (SSM) by providing actionable agricultural practices (e.g. harvest) into vineyard management, guiding winemakers to implement tailored interventions based on metabolic profiles rather than only cultivar characteristics. This precision viticulture (PV) approach enhances wine quality and production efficiency by aligning vineyard practices with specific wine quality goals.

2024

Precision Fertilization: A critical review analysis on sensing technologies for nitrogen, phosphorous and potassium quantification

Authors
Silva, FM; Queiros, C; Pereira, M; Pinho, T; Barroso, T; Magalhaes, S; Boaventura, J; Santos, F; Cunha, M; Martins, RC;

Publication
COMPUTERS AND ELECTRONICS IN AGRICULTURE

Abstract
Fertilization is paramount for agriculture productivity and food security. Plant nutrition pre-established recipes and nutrient uptake are rarely managed by changing the fertilizer composition at the different stages of the plant life cycle. Herein we perform a literature review analysis - since the year 2000 and onwards - of the state-of-the-art capabilities of Nitrogen, Phosphorous, and Potassium (NPK) sensors for liquid fertilizers ( e.g. , hydroponics). From the initial search hits of 1660 results, only 53 publications had relevant information for this topic; from these, only 9 had NPK quantitative information. Qualitative analysis was performed by determining the number of publications for each nutrient, according to sample complexity and existing single, multiplexed or hybrid technologies. Quantitative assessment was performed by extracting the bias and linearity, the limit of detection and concentration ranges of sensor operation, framed into the context of the sensor technology development stage and sample compositional complexity. The most common technologies are colorimetry, ionselective electrodes, optrodes, chemosensors, and optical spectroscopy. The most abundant technologies are for nitrate quantification, from which ion-selective electrodes are the most widely used technology, and sensors for phosphate quantification are the less developed. Most are at low technological levels of development, not dealing with the complexity of agriculture samples due to matrix effects and interference. Measuring the fertilizer composition, nutrient uptake, the state of the chemical network, and controlling the release of nutrients using new functional materials, is one of the most important challenges ahead for the existence of precision fertilization. Intelligent sensing and smart materials are today the most successful strategy for dealing with matrix effects and interferences, being led by ion-selective electrodes and spectroscopy technologies.

2024

Towards On-Site Dairy Cow Mastitis Diagnosis in Your Pocket

Authors
Costa, A; Pereira, A; Pinho, L; Gregório, H; Santos, F; Moura, P; Marcos, R; Martins, RC;

Publication
The 4th International Electronic Conference on Biosensors

Abstract

2024

Integrating Spectral Sensing and Systems Biology for Precision Viticulture: Effects of Shade Nets on Grapevine Leaves

Authors
Tosin, R; Portis, I; Rodrigues, L; Gonçalves, I; Barbosa, C; Teixeira, J; Mendes, RJ; Santos, F; Santos, C; Martins, R; Cunha, M;

Publication
HORTICULTURAE

Abstract
This study investigates how grapevines (Vitis vinifera L.) respond to shading induced by artificial nets, focusing on physiological and metabolic changes. Through a multidisciplinary approach, grapevines' adaptations to shading are presented via biochemical analyses and hyperspectral data that are then combined with systems biology techniques. In the study, conducted in a 'Moscatel Galego Branco' vineyard in Portugal's Douro Wine Region during post-veraison, shading was applied and predawn leaf water potential (Psi pd) was then measured to assess water stress. Biochemical analyses and hyperspectral data were integrated to explore adaptations to shading, revealing higher chlorophyll levels (chlorophyll a-b 117.39% higher) and increased Reactive Oxygen Species (ROS) levels in unshaded vines (52.10% higher). Using a self-learning artificial intelligence algorithm (SL-AI), simulations highlighted ROS's role in stress response and accurately predicted chlorophyll a (R2: 0.92, MAPE: 24.39%), chlorophyll b (R2: 0.96, MAPE: 17.61%), and ROS levels (R2: 0.76, MAPE: 52.17%). In silico simulations employing flux balance analysis (FBA) elucidated distinct metabolic phenotypes between shaded and unshaded vines across cellular compartments. Integrating these findings provides a systems biology approach for understanding grapevine responses to environmental stressors. The leveraging of advanced omics technologies and precise metabolic models holds immense potential for untangling grapevine metabolism and optimizing viticultural practices for enhanced productivity and quality.

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