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Publications

Publications by BIO

2016

Hessian based approaches for 3D lung nodule segmentation

Authors
Goncalves, L; Novo, J; Campilho, A;

Publication
EXPERT SYSTEMS WITH APPLICATIONS

Abstract
In the design of computer-aided diagnosis systems for lung cancer diagnosis, an appropriate and accurate segmentation of the pulmonary nodules in computerized tomography (CT) is one of the most relevant and difficult tasks. An accurate segmentation is crucial for the posterior measurement of nodule characteristics and for lung cancer diagnosis. This paper proposes different approaches that use Hessian-based strategies for lung nodule segmentation in chest CT scans. We propose a multiscale segmentation process that uses the central medialness adaptive principle, a Hessian-based strategy that was originally formulated for tubular extraction but it also provides good segmentation results in blob-like structures as is the case of lung nodules. We compared this proposal with a well established Hessian-based strategy that calculates the Shape Index (SI) and Curvedness (CV). We adapted the SI and CV approach for multiscale nodule segmentation. Moreover, we propose the combination of both strategies by combining the results, in order to take benefit of the advantages of both strategies. Different cases with pulmonary nodules from the Lung Image Database Consortium and Image Database Resource Initiative (LIDC-IDRI) database were taken and used to analyze and validate the approaches. The chest CT images present a large variability in nodule characteristics and image conditions. Our proposals provide an accurate lung nodule segmentation, similar to radiologists performance. Our Hessian-based approaches were validated with 569 solid and mostly solid nodules demonstrating that these novel strategies have good results when compared with the radiologists segmentations, providing accurate pulmonary nodule volumes for posterior characterization and appropriate diagnosis.

2016

Spatiotemporal Control of Forkhead Binding to DNA Regulates the Meiotic Gene Expression Program

Authors
Alves Rodrigues, I; Ferreira, PG; Moldon, A; Vivancos, AP; Hidalgo, E; Guigo, R; Ayte, J;

Publication
CELL REPORTS

Abstract
Meiosis is a differentiated program of the cell cycle that is characterized by high levels of recombination followed by two nuclear divisions. In fission yeast, the genetic program during meiosis is regulated at multiple levels, including transcription, mRNA stabilization, and splicing. Mei4 is a forkhead transcription factor that controls the expression of mid-meiotic genes. Here, we describe that Fkh2, another forkhead transcription factor that is essential for mitotic cell-cycle progression, also plays a pivotal role in the control of meiosis. Fkh2 binding preexists in most Mei4-dependent genes, inhibiting their expression. During meiosis, Fkh2 is phosphorylated in a CDK/Cig2-dependent manner, decreasing its affinity for DNA, which creates a window of opportunity for Mei4 binding to its target genes. We propose that Fkh2 serves as a placeholder until the later appearance of Mei4 with a higher affinity for DNA that induces the expression of a subset of meiotic genes.

2016

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing

Authors
Ferreira, PG; Oti, M; Barann, M; Wieland, T; Ezquina, S; Friedländer, MR; Rivas, MA; Esteve-Codina, A; Estivill, X; Guigó, R; Dermitzakis, E; Antonarakis, S; Meitinger, T; Strom, TM; Palotie, A; François Deleuze, J; Sudbrak, R; Lerach, H; Gut, I; Syvänen, A; Gyllensten, U; Schreiber, S; Rosenstiel, P; Brunner, H; Veltman, J; Hoen, PA; Jan van Ommen, G; Carracedo, A; Brazma, A; Flicek, P; Cambon-Thomsen, A; Mangion, J; Bentley, D; Hamosh, A; Rosenstiel, P; Strom, TM; Lappalainen, T; Guigó, R; Sammeth, M;

Publication
SCIENTIFIC REPORTS

Abstract
Recent advances in the cost-efficiency of sequencing technologies enabled the combined DNA-and RNA-sequencing of human individuals at the population-scale, making genome-wide investigations of the inter-individual genetic impact on gene expression viable. Employing mRNA-sequencing data from the Geuvadis Project and genome sequencing data from the 1000 Genomes Project we show that the computational analysis of DNA sequences around splice sites and poly-A signals is able to explain several observations in the phenotype data. In contrast to widespread assessments of statistically significant associations between DNA polymorphisms and quantitative traits, we developed a computational tool to pinpoint the molecular mechanisms by which genetic markers drive variation in RNA-processing, cataloguing and classifying alleles that change the affinity of core RNA elements to their recognizing factors. The in silico models we employ further suggest RNA editing can moonlight as a splicing-modulator, albeit less frequently than genomic sequence diversity. Beyond existing annotations, we demonstrate that the ultra-high resolution of RNA-Seq combined from 462 individuals also provides evidence for thousands of bona fide novel elements of RNA processing-alternative splice sites, introns, and cleavage sites-which are often rare and lowly expressed but in other characteristics similar to their annotated counterparts.

2016

Effects of perceived stress and fatigue in Firefighters cognitive performance: a pilot study

Authors
Rodrigues, S; Paiva, J; Pimentel, G; Silva Cunha, JPS;

Publication
SHO2016: INTERNATIONAL SYMPOSIUM ON OCCUPATIONAL SAFETY AND HYGIENE

Abstract
Firefighting is a hazardous occupation. Firefighters are commonly subjected to high levels of stress and fatigue that could interfere with their ability to take decisions under pressure. Based on this assumption, a laboratory protocol was conducted among 10 Portuguese firefighters in order to address their stress and mental fatigue levels and its impact on cognitive performance. A 2-Choice Reaction Time Task was used to measure cognitive performance (before and after a stress condition) and a psychosocial stress paradigm was used to assess stress. Visual Analogue Scales were also used to measure perceived stress and mental fatigue. Results suggested that firefighters felt more fatigued at the end of the protocol, however their performance only decreased in the first reaction time task. Furthermore, findings suggested that stress improved firefighters reaction times, however when stress levels increased, performance decreased. This suggests the need to better understand firefighters optimal stress levels and fatigue, in order to promote their health and work safety, by improving their performance under demanding situations.

2016

Machine learning for medical applications

Authors
Canedo, VB; Remeseiro, B; Betanzos, AA; Campilho, A;

Publication
24th European Symposium on Artificial Neural Networks, ESANN 2016, Bruges, Belgium, April 27-29, 2016

Abstract

2016

Optical clearing mechanisms characterization in muscle

Authors
Oliveira, L; Carvalho, MI; Nogueira, E; Tuchin, VV;

Publication
JOURNAL OF INNOVATIVE OPTICAL HEALTH SCIENCES

Abstract
Optical immersion clearing is a technique that has been widely studied for more than two decades and that is used to originate a temporary transparency effect in biological tissues. If applied in cooperation with clinical methods it provides optimization of diagnosis and treatment procedures. This technique turns biological tissues more transparent through two main mechanisms - tissue dehydration and refractive index (RI) matching between tissue components. Such matching is obtained by partial replacement of interstitial water by a biocompatible agent that presents higher RI and it can be completely reversible by natural rehydration in vivo or by assisted rehydration in ex vivo tissues. Experimental data to characterize and discriminate between the two mechanisms and to find new ones are necessary. Using a simple method, based on collimated transmittance and thickness measurements made from muscle samples under treatment, we have estimated the diffusion properties of glucose, ethylene glycol (EG) and water that were used to perform such characterization and discrimination. Comparing these properties with data from literature that characterize their diffusion in water we have observed that muscle cell membrane permeability limits agent and water diffusion in the muscle. The same experimental data has allowed to calculate the optical clearing (OC) efficiency and make an interpretation of the internal changes that occurred in muscle during the treatments. The same methodology can now be used to perform similar studies with other agents and in other tissues in order to solve engineering problems at design of inexpensive and robust technologies for a considerable improvement of optical tomographic techniques with better contrast and in-depth imaging.

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