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Publications

Publications by BIO

2019

Optical fiber-based sensing method for nanoparticle detection through supervised back-scattering analysis: a potential contributor for biomedicine

Authors
Paiva, JS; Jorge, PAS; Ribeiro, RSR; Sampaio, P; Rosa, CC; Cunha, JPS;

Publication
INTERNATIONAL JOURNAL OF NANOMEDICINE

Abstract
Background: In view of the growing importance of nanotechnologies, the detection/identification of nanoparticles type has been considered of utmost importance. Although the characterization of synthetic/organic nanoparticles is currently considered a priority (eg, drug delivery devices, nanotextiles, theranostic nanoparticles), there are many examples of "naturally" generated nanostructures - for example, extracellular vesicles (EVs), lipoproteins, and virus - that provide useful information about human physiology or clinical conditions. For example, the detection of tumor-related exosomes, a specific type of EVs, in circulating fluids has been contributing to the diagnosis of cancer in an early stage. However, scientists have struggled to find a simple, fast, and low-cost method to accurately detect/identify these nanoparticles, since the majority of them have diameters between 100 and 150 nm, thus being far below the diffraction limit. Methods: This study investigated if, by projecting the information provided from short-term portions of the back-scattered laser light signal collected by a polymeric lensed optical fiber tip dipped into a solution of synthetic nanoparticles into a lower features dimensional space, a discriminant function is able to correctly detect the presence of 100 nm synthetic nanoparticles in distilled water, in different concentration values. Results and discussion: This technique ensured an optimal performance (100% accuracy) in detecting nanoparticles for a concentration above or equal to 3.89 mu g/mL (8.74E+10 particles/mL), and a performance of 90% for concentrations below this value and higher than 1.22E-03 mu g/mL (2.74E+07 particles/mL), values that are compatible with human plasmatic levels of tumor-derived and other types of EVs, as well as lipoproteins currently used as potential biomarkers of cardiovascular diseases. Conclusion: The proposed technique is able to detect synthetic nanoparticles whose dimensions are similar to EVs and other "clinically" relevant nanostructures, and in concentrations equivalent to the majority of cell-derived, platelet-derived EVs and lipoproteins physiological levels. This study can, therefore, provide valuable insights towards the future development of a device for EVs and other biological nanoparticles detection with innovative characteristics.

2019

BACH: Grand challenge on breast cancer histology images

Authors
Aresta, G; Araujo, T; Kwok, S; Chennamsetty, SS; Safwan, M; Alex, V; Marami, B; Prastawa, M; Chan, M; Donovan, M; Fernandez, G; Zeineh, J; Kohl, M; Walz, C; Ludwig, F; Braunewell, S; Baust, M; Vu, QD; To, MNN; Kim, E; Kwak, JT; Galal, S; Sanchez Freire, V; Brancati, N; Frucci, M; Riccio, D; Wang, YQ; Sun, LL; Ma, KQ; Fang, JN; Kone, ME; Boulmane, LS; Campilho, ARLO; Eloy, CTRN; Polonia, AONO; Aguiar, PL;

Publication
MEDICAL IMAGE ANALYSIS

Abstract
Breast cancer is the most common invasive cancer in women, affecting more than 10% of women worldwide. Microscopic analysis of a biopsy remains one of the most important methods to diagnose the type of breast cancer. This requires specialized analysis by pathologists, in a task that i) is highly time and cost-consuming and ii) often leads to nonconsensual results. The relevance and potential of automatic classification algorithms using hematoxylin-eosin stained histopathological images has already been demonstrated, but the reported results are still sub-optimal for clinical use. With the goal of advancing the state-of-the-art in automatic classification, the Grand Challenge on BreAst Cancer Histology images (BACH) was organized in conjunction with the 15th International Conference on Image Analysis and Recognition (ICIAR 2018). BACH aimed at the classification and localization of clinically relevant histopathological classes in microscopy and whole-slide images from a large annotated dataset, specifically compiled and made publicly available for the challenge. Following a positive response from the scientific community, a total of 64 submissions, out of 677 registrations, effectively entered the competition. The submitted algorithms improved the state-of-the-art in automatic classification of breast cancer with microscopy images to an accuracy of 87%. Convolutional neuronal networks were the most successful methodology in the BACH challenge. Detailed analysis of the collective results allowed the identification of remaining challenges in the field and recommendations for future developments. The BACH dataset remains publicly available as to promote further improvements to the field of automatic classification in digital pathology.

2019

Expert Crowdsourcing for Semantic Annotation of Atmospheric Phenomena

Authors
Liberato, M; Paredes, H; Ramos, A; Reis, A; Hénin, R; Barroso, J;

Publication

Abstract

2019

TTR-FAP Progression Evaluation Based on Gait Analysis Using a Single RGB-D Camera

Authors
Vilas Boas, MD; Rocha, AP; Pereira Choupina, HMP; Cardoso, M; Fernandes, JM; Coelho, T; Silva Cunha, JPS;

Publication
2019 41ST ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY (EMBC)

Abstract
Transthyretin Familial Amyloid Polyneuropathy (TTR-FAP) is a rare and disabling neurological disorder caused by, a mutation of the transthyretin gene. One of the disease's characteristics that mostly affects patients' quality of life is its influence on locomotion, with a variable evolution timing. Quantitative motion analysis is useful for assessing motor function, including gait, in diseases affecting movement. However, it is still an evolving field, especially in TTR-FAP, with only a few available studies. A single markerless RGB-D camera pros ides 3-D body joint data in a less expensive, more portable and less intrusive way than reference multi-camera marker-based systems for motion capture. In this contribution, we investigate if a gait analysis system based on a RGB-D camera can be used to detect gait changes over time for a given TTR-FAP patient. 3-D data provided by that system and a reference system were acquired from six TTR-FAP patients, while performing a simple gait task, once and then a year and a half later. For each gait cycle and system, several gait parameters were computed. For each patient, we investigated if the RBG-D camera system is able to detect the existence or not of statistically significant differences between the two different acquisitions (separated by 1.5 years of disease evolution), in a similar way to the reference system. The obtained results show the potential of using a single RGB-D camera to detect relevant changes in spatiotemporal gait parameters (e.g., stride duration and stride length), during TTR-FAP patient follow-up.

2019

Humidity sensor based on optical fiber coated with agarose gel

Authors
Novais, S; Ferreira, MS; Pinto, JL;

Publication
OPTICAL SENSORS 2019

Abstract
A reflective fiber optic sensor based on multimode interference for the measurement of relative humidity (RH) is proposed and experimentally demonstrated. The proposed probe is fabricated by fusion-splicing, approximately 30 mm long coreless fiber section to a single mode fiber. A hydrophilic agarose gel is coated on the coreless fiber, using the dip coating technique. When the incident light comes from the SMF to the CSF, the high-order modes are excited and propagate within the CSF. These excited modes interfere with one another as they propagate along whole CSF length, giving rise to a multimode interference (MMI). Since the effective refractive index of the agarose gel changes with the ambient relative humidity, as the environmental refractive index changes, the propagation constants for each guided mode within the CSF will change too, which leads to shifts in the output spectra. The proposed sensor has a great potential in real time RH monitoring, exhibiting a large range of operation with good stability. For RH variations in the range between 60 %RH and 98.5 %RH, the sensor presents a maximum sensitivity of 44.2 pm/%RH, and taking in consideration the interrogation system, a resolution of 1.1%RH is acquired. This sensor can be of interest for applications where a control of high levels of relative humidity is required.

2019

A Dynamic Mode Decomposition Approach with Hankel Blocks to Forecast Multi-Channel Temporal Series

Authors
Filho, EV; Dos Santos, PL;

Publication
IEEE Control Systems Letters

Abstract
Forecasting is a task with many concerns, such as the size, quality, and behavior of the data, the computing power to do it, etc. This letter proposes the dynamic mode decomposition (DMD) as a tool to predict the annual air temperature and the sales of a stores' chain. The DMD decomposes the data into its principal modes, which are estimated from a training data set. It is assumed that the data is generated by a linear time-invariant high order autonomous system. These modes are useful to find the way the system behaves and to predict its future states, without using all the available data, even in a noisy environment. The Hankel block allows the estimation of hidden oscillatory modes, by increasing the order of the underlying dynamical system. The proposed method was tested in a case study consisting of the long term prediction of the weekly sales of a chain of stores. The performance assessment was based on the best fit percentage index. The proposed method is compared with three neural network-based predictors. © 2017 IEEE.

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