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Publicações

Publicações por BIO

2021

Unravelling Plant-Pathogen Interactions: Proximal Optical Sensing as an Effective Tool for Early Detect Plant Diseases

Autores
Reis-Pereira, M; Martins, RC; Silva, AF; Tavares, F; Santos, F; Cunha, M;

Publicação
Chemistry Proceedings

Abstract
This study analyzed the potential of proximal optical sensing as an effective approach for early disease detection. A compact, modular sensing system, combining direct UV–Vis spectroscopy with optical fibers, supported by a principal component analysis (PCA), was applied to evaluate the modifications promoted by the bacteria Xanthomonas euvesicatoria in tomato leaves (cv. cherry). Plant infection was achieved by spraying a bacterial suspension (108 CFU mL-1) until run-off occurred, and a similar approach was followed for the control group, where only water was applied. A total of 270 spectral measurements were performed on leaves, on five different time instances, including pre- and post-inoculation measurements. PCA was then applied to the acquired data from both healthy and inoculated leaves, which allowed their distinction and differentiation, three days after inoculation, when unhealthy plants were still asymptomatic.

2021

Systematic Comparison of Left Ventricular Geometry Between 3D-Echocardiography and Cardiac Magnetic Resonance Imaging

Autores
Zhao, D; Quill, GM; Gilbert, K; Wang, VY; Houle, HC; Legget, ME; Ruygrok, PN; Doughty, RN; Pedrosa, J; D'hooge, J; Young, AA; Nash, MP;

Publicação
FRONTIERS IN CARDIOVASCULAR MEDICINE

Abstract
Aims: Left ventricular (LV) volumes estimated using three-dimensional echocardiography (3D-echo) have been reported to be smaller than those measured using cardiac magnetic resonance (CMR) imaging, but the underlying causes are not well-understood. We investigated differences in regional LV anatomy derived from these modalities and related subsequent findings to image characteristics.

Methods and Results: Seventy participants (18 patients and 52 healthy participants) were imaged with 3D-echo and CMR (<1 h apart). Three-dimensional left ventricular models were constructed at end-diastole (ED) and end-systole (ES) from both modalities using previously validated software, enabling the fusion of CMR with 3D-echo by rigid registration. Regional differences were evaluated as mean surface distances for each of the 17 American Heart Association segments, and by comparing contours superimposed on images from each modality. In comparison to CMR-derived models, 3D-echo models underestimated LV end-diastolic volume (EDV) by -16 +/- 22, -1 +/- 25, and -18 +/- 24 ml across three independent analysis methods. Average surface distance errors were largest in the basal-anterolateral segment (11-15 mm) and smallest in the mid-inferoseptal segment (6 mm). Larger errors were associated with signal dropout in anterior regions and the appearance of trabeculae at the lateral wall.

Conclusions: Fusion of CMR and 3D-echo provides insight into the causes of volume underestimation by 3D-echo. Systematic signal dropout and differences in appearances of trabeculae lead to discrepancies in the delineation of LV geometry at anterior and lateral regions. A better understanding of error sources across modalities may improve correlation of clinical indices between 3D-echo and CMR.

2021

Sharing Biomedical Data: Strengthening AI Development in Healthcare

Autores
Pereira, T; Morgado, J; Silva, F; Pelter, MM; Dias, VR; Barros, R; Freitas, C; Negrao, E; de Lima, BF; da Silva, MC; Madureira, AJ; Ramos, I; Hespanhol, V; Costa, JL; Cunha, A; Oliveira, HP;

Publicação
HEALTHCARE

Abstract
Artificial intelligence (AI)-based solutions have revolutionized our world, using extensive datasets and computational resources to create automatic tools for complex tasks that, until now, have been performed by humans. Massive data is a fundamental aspect of the most powerful AI-based algorithms. However, for AI-based healthcare solutions, there are several socioeconomic, technical/infrastructural, and most importantly, legal restrictions, which limit the large collection and access of biomedical data, especially medical imaging. To overcome this important limitation, several alternative solutions have been suggested, including transfer learning approaches, generation of artificial data, adoption of blockchain technology, and creation of an infrastructure composed of anonymous and abstract data. However, none of these strategies is currently able to completely solve this challenge. The need to build large datasets that can be used to develop healthcare solutions deserves special attention from the scientific community, clinicians, all the healthcare players, engineers, ethicists, legislators, and society in general. This paper offers an overview of the data limitation in medical predictive models; its impact on the development of healthcare solutions; benefits and barriers of sharing data; and finally, suggests future directions to overcome data limitations in the medical field and enable AI to enhance healthcare. This perspective is dedicated to the technical requirements of the learning models, and it explains the limitation that comes from poor and small datasets in the medical domain and the technical options that try or can solve the problem related to the lack of massive healthcare data.

2021

Chest Radiography Few-Shot Image Synthesis for Automated Pathology Screening Applications

Autores
Sousa, MQE; Pedrosa, J; Rocha, J; Pereira, SC; Mendonça, AM; Campilho, A;

Publicação
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021, Houston, TX, USA, December 9-12, 2021

Abstract
Chest radiography is one of the most ubiquitous imaging modalities, playing an essential role in screening, diagnosis and disease management. However, chest radiography interpretation is a time-consuming and complex task, requiring the availability of experienced radiologists. As such, automated diagnosis systems for pathology detection have been proposed aiming to reduce the burden on radiologists and reduce variability in image interpretation. While promising results have been obtained, particularly since the advent of deep learning, there are significant limitations in the developed solutions, namely the lack of representative data for less frequent pathologies and the learning of biases from the training data, such as patient position, medical devices and other markers as proxies for certain pathologies. The lack of explainability is also a challenge for the adoption of these solutions in clinical practice.Generative adversarial networks could play a significant role as a solution for these challenges as they allow to artificially create new realistic images. This way, new synthetic chest radiography images could be used to increase the prevalence of less represented pathology classes and decrease model biases as well as improving the explainability of automatic decisions by generating samples that serve as examples or counter-examples to the image being analysed, ensuring patient privacy.In this study, a few-shot generative adversarial network is used to generate synthetic chest radiography images. A minimum Fréchet Inception Distance score of 17.83 was obtained, allowing to generate convincing synthetic images. Perceptual validation was then performed by asking multiple readers to classify a mixed set of synthetic and real images. An average accuracy of 83.5% was obtained but a strong dependency on reader experience level was observed. While synthetic images showed structural irregularities, the overall image sharpness was a major factor in the decision of readers. The synthetic images were then validated using a MobileNet abnormality classifier and it was shown that over 99% of images were classified correctly, indicating that the generated images were correctly interpreted by the classifier. Finally, the use of the synthetic images during training of a YOLOv5 pathology detector showed that the addition of the synthetic images led to an improvement of mean average precision of 0.05 across 14 pathologies.In conclusion, the usage of few-shot generative adversarial networks for chest radiography image generation was shown and tested in multiple scenarios, establishing a baseline for future experiments to increase the applicability of generative models in clinical scenarios of automatic CXR screening and diagnosis tools.

2021

Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease

Autores
de Goede, OM; Nachun, DC; Ferraro, NM; Gloudemans, MJ; Rao, AS; Smail, C; Eulalio, TY; Aguet, F; Ng, B; Xu, J; Barbeira, AN; Castel, SE; Kim-Hellmuth, S; Park, Y; Scott, AJ; Strober, BJ; Brown, CD; Wen, X; Hall, IM; Battle, A; Lappalainen, T; Im, HK; Ardlie, KG; Mostafavi, S; Quertermous, T; Kirkegaard, K; Montgomery, SB; Anand, S; Gabriel, S; Getz, GA; Graubert, A; Hadley, K; Handsaker, RE; Huang, KH; Li, X; MacArthur, DG; Meier, SR; Nedzel, JL; Nguyen, DT; Segrè, AV; Todres, E; Balliu, B; Bonazzola, R; Brown, A; Conrad, DF; Cotter, DJ; Cox, N; Das, S; Dermitzakis, ET; Einson, J; Engelhardt, BE; Eskin, E; Flynn, ED; Fresard, L; Gamazon, ER; Garrido-Martín, D; Gay, NR; Guigó, R; Hamel, AR; He, Y; Hoffman, PJ; Hormozdiari, F; Hou, L; Jo, B; Kasela, S; Kashin, S; Kellis, M; Kwong, A; Li, X; Liang, Y; Mangul, S; Mohammadi, P; Muñoz-Aguirre, M; Nobel, AB; Oliva, M; Park, Y; Parsana, P; Reverter, F; Rouhana, JM; Sabatti, C; Saha, A; Stephens, M; Stranger, BE; Teran, NA; Viñuela, A; Wang, G; Wright, F; Wucher, V; Zou, Y; Ferreira, PG; Li, G; Melé, M; Yeger-Lotem, E; Bradbury, D; Krubit, T; McLean, JA; Qi, L; Robinson, K; Roche, NV; Smith, AM; Tabor, DE; Undale, A; Bridge, J; Brigham, LE; Foster, BA; Gillard, BM; Hasz, R; Hunter, M; Johns, C; Johnson, M; Karasik, E; Kopen, G; Leinweber, WF; McDonald, A; Moser, MT; Myer, K; Ramsey, KD; Roe, B; Shad, S; Thomas, JA; Walters, G; Washington, M; Wheeler, J; Jewell, SD; Rohrer, DC; Valley, DR; Davis, DA; Mash, DC; Barcus, ME; Branton, PA; Sobin, L; Barker, LK; Gardiner, HM; Mosavel, M; Siminoff, LA; Flicek, P; Haeussler, M; Juettemann, T; Kent, WJ; Lee, CM; Powell, CC; Rosenbloom, KR; Ruffier, M; Sheppard, D; Taylor, K; Trevanion, SJ; Zerbino, DR; Abell, NS; Akey, J; Chen, L; Demanelis, K; Doherty, JA; Feinberg, AP; Hansen, KD; Hickey, PF; Jasmine, F; Jiang, L; Kaul, R; Kibriya, MG; Li, JB; Li, Q; Lin, S; Linder, SE; Pierce, BL; Rizzardi, LF; Skol, AD; Smith, KS; Snyder, M; Stamatoyannopoulos, J; Tang, H; Wang, M; Carithers, LJ; Guan, P; Koester, SE; Little, AR; Moore, HM; Nierras, CR; Rao, AK; Vaught, JB; Volpi, S;

Publicação
Cell

Abstract
Long non-coding RNA (lncRNA) genes have well-established and important impacts on molecular and cellular functions. However, among the thousands of lncRNA genes, it is still a major challenge to identify the subset with disease or trait relevance. To systematically characterize these lncRNA genes, we used Genotype Tissue Expression (GTEx) project v8 genetic and multi-tissue transcriptomic data to profile the expression, genetic regulation, cellular contexts, and trait associations of 14,100 lncRNA genes across 49 tissues for 101 distinct complex genetic traits. Using these approaches, we identified 1,432 lncRNA gene-trait associations, 800 of which were not explained by stronger effects of neighboring protein-coding genes. This included associations between lncRNA quantitative trait loci and inflammatory bowel disease, type 1 and type 2 diabetes, and coronary artery disease, as well as rare variant associations to body mass index.

2021

Supporting the Assessment of Hereditary Transthyretin Amyloidosis Patients Based On 3-D Gait Analysis and Machine Learning

Autores
Vilas Boas, MD; Rocha, AP; Cardoso, MN; Fernandes, JM; Coelho, T; Cunha, JPS;

Publicação
IEEE TRANSACTIONS ON NEURAL SYSTEMS AND REHABILITATION ENGINEERING

Abstract
Hereditary Transthyretin Amyloidosis (vATTR-V30M) is a rare and highly incapacitating sensorimotor neuropathy caused by an inherited mutation (Val30Met), which typically affects gait, among other symptoms. In this context, we investigated the possibility of using machine learning (ML) techniques to build a model(s) that can be used to support the detection of the Val30Met mutation (possibility of developing the disease), as well as symptom onset detection for the disease, given the gait characteristics of a person. These characteristics correspond to 24 gait parameters computed from 3-D body data, provided by a Kinect v2 camera, acquired from a person while walking towards the camera. To build the model(s), different ML algorithms were explored: k-nearest neighbors, decision tree, random forest, support vector machines (SVM), and multilayer perceptron. For a dataset corresponding to 66 subjects (25 healthy controls, 14 asymptomatic mutation carriers, and 27 patients) and several gait cycles per subject, we were able to obtain a model that distinguishes between controls and vATTR-V30M mutation carriers (with or without symptoms) with a mean accuracy of 92% (SVM). We also obtained a model that distinguishes between asymptomatic and symptomatic carriers with a mean accuracy of 98% (SVM). These results are very relevant, since this is the first study that proposes a ML approach to support vATTR-V30M patient assessment based on gait, being a promising foundation for the development of a computer-aided diagnosis tool to help clinicians in the identification and follow-up of this disease. Furthermore, the proposed method may also be used for other neuropathies.

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