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Publicações

2017

Massive Data Visualization Analysis Analysis of current visualization techniques and main challenges for the future

Autores
Perez Cota, MP; Diaz Rodriguez, MD; Ramon Gonzalez Castro, MR; Moreira Goncalves, RMM;

Publicação
2017 12TH IBERIAN CONFERENCE ON INFORMATION SYSTEMS AND TECHNOLOGIES (CISTI)

Abstract
The big amount of data generated nowadays are being used by Big Data tools to generate knowledge and to facilitate the decision-making. However, this situation creates a new challenge: how to visualize all these data without losing mid/long term crucial information. The purpose of this article is to analyze the state of the art on massive data visualization, main problems and challenges of information representation current techniques as well as the evolution of the tools and the future of them, in other words, new functionalities to offer.

2017

mu SmartScope: 3D-printed Smartphone Microscope with Motorized Automated Stage

Autores
Rosado, L; Oliveira, J; Vasconcelos, MJM; da Costa, JMC; Elias, D; Cardoso, JS;

Publicação
PROCEEDINGS OF THE 10TH INTERNATIONAL JOINT CONFERENCE ON BIOMEDICAL ENGINEERING SYSTEMS AND TECHNOLOGIES, VOL 1: BIODEVICES

Abstract
Microscopic examination is currently the gold standard test for diagnosis of several neglected tropical diseases. However, reliable identification of parasitic infections requires in-depth train and access to proper equipment for subsequent microscopic analysis. These requirements are closely related with the increasing interest in the development of computer-aided diagnosis systems, and Mobile Health is starting to play an important role when it comes to health in Africa, allowing for distributed solutions that provide access to complex diagnosis even in rural areas. In this paper, we present a 3D-printed microscope that can easily be attached to a wide range of mobile devices models. To the best of our knowledge, this is the first proposed smartphone-based alternative to conventional microscopy that allows autonomous acquisition of a pre-defined number of images at 1000x magnification with suitable resolution, by using a motorized automated stage fully powered and controlled by a smartphone, without the need of manual focus of the smear slide. Reference smears slides with different parasites were used to test the device. The acquired images showed that was possible to visually detect those agents, which clearly illustrate the potential that this device can have, specially in developing countries with limited access to healthcare services.

2017

Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancer

Autores
Fonseca, NA; He, Y; Greger, L; Brazma, A; Zhang, Z; - PCAWG-3,;

Publicação

Abstract
Gene fusions are an important class of cancer-driving events with therapeutic and diagnostic values, yet their underlying genetic mechanisms have not been systematically characterized. Here by combining RNA and whole genome DNA sequencing data from 1188 donors across 27 cancer types we obtained a list of 3297 high-confidence tumour-specific gene fusions, 82% of which had structural variant (SV) support and 2372 of which were novel. Such a large collection of RNA and DNA alterations provides the first opportunity to systematically classify the gene fusions at a mechanistic level. While many could be explained by single SVs, numerous fusions involved series of structural rearrangements and thus are composite fusions. We discovered 75 fusions of a novel class of inter-chromosomal composite fusions, termed bridged fusions, in which a third genomic location bridged two different genes. In addition, we identified 522 fusions involving non-coding genes and 157 ORF-retaining fusions, in which the complete open reading frame of one gene was fused to the UTR region of another. Although only a small proportion (5%) of the discovered fusions were recurrent, we found a set of highly recurrent fusion partner genes, which exhibited strong 5' or 3' bias and were significantly enriched for cancer genes. Our findings broaden the view of the gene fusion landscape and reveal the general properties of genetic alterations underlying gene fusions for the first time.

2017

Enriching conflict resolution environments with the provision of context information

Autores
Carneiro, D; Gomes, M; Costa, A; Novais, P; Neves, J;

Publicação
EXPERT SYSTEMS

Abstract
It is a common affair to settle disputes out of courts nowadays, through negotiation, mediation or any other mean. This has also been implemented over telecommunication means under the so-called Online Dispute Resolution methods. However, this new technology-supported approach is impersonal and cold, leaving aside important issues such as the disputants' body language, stress level or emotional response while being based on forms, e-mails or chat rooms. To overcome this shortcoming, in this paper, it is proposed the creation of intelligent environments for conflict resolution that can complement the existing tools with important knowledge about the context of interaction. This will allow decision-makers to take better framed decisions based not only on figures but also on important contextual information, similar to what happens when parties communicate in the physical presence of each other.

2017

On the Implementation of a Cloud-Based Computing Test Bench Environment for Prolog Systems

Autores
Goncalves, R; Areias, M; Rocha, R;

Publicação
INFORMATION

Abstract
Software testing and benchmarking are key components of the software development process. Nowadays, a good practice in large software projects is the continuous integration (CI) software development technique. The key idea of CI is to let developers integrate their work as they produce it, instead of performing the integration at the end of each software module. In this paper, we extend a previous work on a benchmark suite for the YAP Prolog system, and we propose a fully automated test bench environment for Prolog systems, named Yet Another Prolog Test Bench Environment (YAPTBE), aimed to assist developers in the development and CI of Prolog systems. YAPTBE is based on a cloud computing architecture and relies on the Jenkins framework as well as a new Jenkins plugin to manage the underlying infrastructure. We present the key design and implementation aspects of YAPTBE and show its most important features, such as its graphical user interface (GUI) and the automated process that builds and runs Prolog systems and benchmarks.

2017

Is Portugal's forest transition going up in smoke?

Autores
Oliveira, TM; Guiomar, N; Oliveira Baptista, FO; Pereira, JMC; Claro, J;

Publicação
LAND USE POLICY

Abstract
The turnarounds from decrease to expansion in forest areas that took place during the last century have been examined through the lens of forest transition theory (FTT). Among temperate and Mediterranean European countries that have seen an expansion of forest cover, Portugal stands out as the only case in which this trend has recently been reverted. In this study, we explicitly map and document the forest transition (FT) in the country over the period 1907-2006, and investigate when and where forest transition happened de facto, and which were the land use transition pathways that resulted from the shrublands, agriculture, and forest interplay dynamics. After thematic and geometric harmonization of land cover maps from 1907, 1955, 1970, 1990, and 2006, a cluster analysis established four typologies, and a transition matrix was constructed to assess land cover dynamics. We found that up to 1955, FT occurred simultaneously with agricultural expansion, as shrubland areas diminished. Afterwards, with the retraction of agricultural area and the consequential decoupling of forest management from local actors, FT gained momentum and expanded up to the 1990s. While during the first half of the 20th century, forest expansion followed the "Scarcity" and "State Policy" pathways fostered by local socio-ecological feedback loops, throughout the second half of the century forest transition was driven by exogenous socio-economic forces, following "Economic Development" and "Globalization" pathways. We show how, despite these forces, FT can be derailed by endogenous factors such as wildfires, which limited and in some areas even reverted the afforestation process, initiating a deforestation phase. Since the necessary conditions for FT (technology shift, urbanization, agriculture retraction and public afforestation programs) were available in mainland Portugal, we advance the hypothesis that critical wildfire risk governance deficits may have been responsible for arresting FT. Considering the critical role of forests and other wooded areas in supporting climate change mitigation and sustainable development, our work provides useful evidence and insights for public decision makers on previously unaddressed dimensions of FTT.

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